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- PDB-4y4y: T=1 capsid structure of SeMV Ndel65CP fused with B-domain of S. a... -

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Basic information

Entry
Database: PDB / ID: 4y4y
TitleT=1 capsid structure of SeMV Ndel65CP fused with B-domain of S. aureus protein SpA at the N-terminus (C2 crystal form)
ComponentsImmunoglobulin G-binding protein A,Coat protein
KeywordsVIRUS / Coat protein / chimeric VLP / in vitro assembly
Function / homology
Function and homology information


IgG binding / viral capsid / structural molecule activity / extracellular region / metal ion binding
Similarity search - Function
Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain ...Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / Jelly Rolls - #20 / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein A / Capsid protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Sesbania mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGulati, A. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
DST, DBT, J.C Bose India
CitationJournal: Virology / Year: 2015
Title: Structural studies on chimeric Sesbania mosaic virus coat protein: Revisiting SeMV assembly.
Authors: Gulati, A. / Murthy, A. / Abraham, A. / Mohan, K. / Natraj, U. / Savithri, H.S. / Murthy, M.R.
History
DepositionFeb 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein A,Coat protein
B: Immunoglobulin G-binding protein A,Coat protein
C: Immunoglobulin G-binding protein A,Coat protein
D: Immunoglobulin G-binding protein A,Coat protein
E: Immunoglobulin G-binding protein A,Coat protein
F: Immunoglobulin G-binding protein A,Coat protein
G: Immunoglobulin G-binding protein A,Coat protein
H: Immunoglobulin G-binding protein A,Coat protein
I: Immunoglobulin G-binding protein A,Coat protein
J: Immunoglobulin G-binding protein A,Coat protein
K: Immunoglobulin G-binding protein A,Coat protein
L: Immunoglobulin G-binding protein A,Coat protein
M: Immunoglobulin G-binding protein A,Coat protein
N: Immunoglobulin G-binding protein A,Coat protein
O: Immunoglobulin G-binding protein A,Coat protein
P: Immunoglobulin G-binding protein A,Coat protein
Q: Immunoglobulin G-binding protein A,Coat protein
R: Immunoglobulin G-binding protein A,Coat protein
S: Immunoglobulin G-binding protein A,Coat protein
T: Immunoglobulin G-binding protein A,Coat protein
U: Immunoglobulin G-binding protein A,Coat protein
V: Immunoglobulin G-binding protein A,Coat protein
W: Immunoglobulin G-binding protein A,Coat protein
X: Immunoglobulin G-binding protein A,Coat protein
Y: Immunoglobulin G-binding protein A,Coat protein
Z: Immunoglobulin G-binding protein A,Coat protein
a: Immunoglobulin G-binding protein A,Coat protein
b: Immunoglobulin G-binding protein A,Coat protein
c: Immunoglobulin G-binding protein A,Coat protein
d: Immunoglobulin G-binding protein A,Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)916,87336
Polymers916,29630
Non-polymers5766
Water7,837435
1
A: Immunoglobulin G-binding protein A,Coat protein
B: Immunoglobulin G-binding protein A,Coat protein
C: Immunoglobulin G-binding protein A,Coat protein
D: Immunoglobulin G-binding protein A,Coat protein
E: Immunoglobulin G-binding protein A,Coat protein
F: Immunoglobulin G-binding protein A,Coat protein
G: Immunoglobulin G-binding protein A,Coat protein
H: Immunoglobulin G-binding protein A,Coat protein
I: Immunoglobulin G-binding protein A,Coat protein
J: Immunoglobulin G-binding protein A,Coat protein
K: Immunoglobulin G-binding protein A,Coat protein
L: Immunoglobulin G-binding protein A,Coat protein
M: Immunoglobulin G-binding protein A,Coat protein
N: Immunoglobulin G-binding protein A,Coat protein
O: Immunoglobulin G-binding protein A,Coat protein
P: Immunoglobulin G-binding protein A,Coat protein
Q: Immunoglobulin G-binding protein A,Coat protein
R: Immunoglobulin G-binding protein A,Coat protein
S: Immunoglobulin G-binding protein A,Coat protein
T: Immunoglobulin G-binding protein A,Coat protein
U: Immunoglobulin G-binding protein A,Coat protein
V: Immunoglobulin G-binding protein A,Coat protein
W: Immunoglobulin G-binding protein A,Coat protein
X: Immunoglobulin G-binding protein A,Coat protein
Y: Immunoglobulin G-binding protein A,Coat protein
Z: Immunoglobulin G-binding protein A,Coat protein
a: Immunoglobulin G-binding protein A,Coat protein
b: Immunoglobulin G-binding protein A,Coat protein
c: Immunoglobulin G-binding protein A,Coat protein
d: Immunoglobulin G-binding protein A,Coat protein
hetero molecules

A: Immunoglobulin G-binding protein A,Coat protein
B: Immunoglobulin G-binding protein A,Coat protein
C: Immunoglobulin G-binding protein A,Coat protein
D: Immunoglobulin G-binding protein A,Coat protein
E: Immunoglobulin G-binding protein A,Coat protein
F: Immunoglobulin G-binding protein A,Coat protein
G: Immunoglobulin G-binding protein A,Coat protein
H: Immunoglobulin G-binding protein A,Coat protein
I: Immunoglobulin G-binding protein A,Coat protein
J: Immunoglobulin G-binding protein A,Coat protein
K: Immunoglobulin G-binding protein A,Coat protein
L: Immunoglobulin G-binding protein A,Coat protein
M: Immunoglobulin G-binding protein A,Coat protein
N: Immunoglobulin G-binding protein A,Coat protein
O: Immunoglobulin G-binding protein A,Coat protein
P: Immunoglobulin G-binding protein A,Coat protein
Q: Immunoglobulin G-binding protein A,Coat protein
R: Immunoglobulin G-binding protein A,Coat protein
S: Immunoglobulin G-binding protein A,Coat protein
T: Immunoglobulin G-binding protein A,Coat protein
U: Immunoglobulin G-binding protein A,Coat protein
V: Immunoglobulin G-binding protein A,Coat protein
W: Immunoglobulin G-binding protein A,Coat protein
X: Immunoglobulin G-binding protein A,Coat protein
Y: Immunoglobulin G-binding protein A,Coat protein
Z: Immunoglobulin G-binding protein A,Coat protein
a: Immunoglobulin G-binding protein A,Coat protein
b: Immunoglobulin G-binding protein A,Coat protein
c: Immunoglobulin G-binding protein A,Coat protein
d: Immunoglobulin G-binding protein A,Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,833,74672
Polymers1,832,59360
Non-polymers1,15312
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area228640 Å2
ΔGint-1149 kcal/mol
Surface area305620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)288.181, 193.040, 189.192
Angle α, β, γ (deg.)90.000, 124.370, 90.000
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112A
212M
113A
213N
114A
214O
115A
215P
116A
216Q
117A
217R
118A
218S
119A
219T
120A
220U
121A
221V
122A
222W
123A
223X
124A
224Y
125A
225Z
126A
226a
127A
227b
128A
228c
129A
229d
130B
230C
131B
231D
132B
232E
133B
233F
134B
234G
135B
235H
136B
236I
137B
237J
138B
238K
139B
239L
140B
240M
141B
241N
142B
242O
143B
243P
144B
244Q
145B
245R
146B
246S
147B
247T
148B
248U
149B
249V
150B
250W
151B
251X
152B
252Y
153B
253Z
154B
254a
155B
255b
156B
256c
157B
257d
158C
258D
159C
259E
160C
260F
161C
261G
162C
262H
163C
263I
164C
264J
165C
265K
166C
266L
167C
267M
168C
268N
169C
269O
170C
270P
171C
271Q
172C
272R
173C
273S
174C
274T
175C
275U
176C
276V
177C
277W
178C
278X
179C
279Y
180C
280Z
181C
281a
182C
282b
183C
283c
184C
284d
185D
285E
186D
286F
187D
287G
188D
288H
189D
289I
190D
290J
191D
291K
192D
292L
193D
293M
194D
294N
195D
295O
196D
296P
197D
297Q
198D
298R
199D
299S
1100D
2100T
1101D
2101U
1102D
2102V
1103D
2103W
1104D
2104X
1105D
2105Y
1106D
2106Z
1107D
2107a
1108D
2108b
1109D
2109c
1110D
2110d
1111E
2111F
1112E
2112G
1113E
2113H
1114E
2114I
1115E
2115J
1116E
2116K
1117E
2117L
1118E
2118M
1119E
2119N
1120E
2120O
1121E
2121P
1122E
2122Q
1123E
2123R
1124E
2124S
1125E
2125T
1126E
2126U
1127E
2127V
1128E
2128W
1129E
2129X
1130E
2130Y
1131E
2131Z
1132E
2132a
1133E
2133b
1134E
2134c
1135E
2135d
1136F
2136G
1137F
2137H
1138F
2138I
1139F
2139J
1140F
2140K
1141F
2141L
1142F
2142M
1143F
2143N
1144F
2144O
1145F
2145P
1146F
2146Q
1147F
2147R
1148F
2148S
1149F
2149T
1150F
2150U
1151F
2151V
1152F
2152W
1153F
2153X
1154F
2154Y
1155F
2155Z
1156F
2156a
1157F
2157b
1158F
2158c
1159F
2159d
1160G
2160H
1161G
2161I
1162G
2162J
1163G
2163K
1164G
2164L
1165G
2165M
1166G
2166N
1167G
2167O
1168G
2168P
1169G
2169Q
1170G
2170R
1171G
2171S
1172G
2172T
1173G
2173U
1174G
2174V
1175G
2175W
1176G
2176X
1177G
2177Y
1178G
2178Z
1179G
2179a
1180G
2180b
1181G
2181c
1182G
2182d
1183H
2183I
1184H
2184J
1185H
2185K
1186H
2186L
1187H
2187M
1188H
2188N
1189H
2189O
1190H
2190P
1191H
2191Q
1192H
2192R
1193H
2193S
1194H
2194T
1195H
2195U
1196H
2196V
1197H
2197W
1198H
2198X
1199H
2199Y
1200H
2200Z
1201H
2201a
1202H
2202b
1203H
2203c
1204H
2204d
1205I
2205J
1206I
2206K
1207I
2207L
1208I
2208M
1209I
2209N
1210I
2210O
1211I
2211P
1212I
2212Q
1213I
2213R
1214I
2214S
1215I
2215T
1216I
2216U
1217I
2217V
1218I
2218W
1219I
2219X
1220I
2220Y
1221I
2221Z
1222I
2222a
1223I
2223b
1224I
2224c
1225I
2225d
1226J
2226K
1227J
2227L
1228J
2228M
1229J
2229N
1230J
2230O
1231J
2231P
1232J
2232Q
1233J
2233R
1234J
2234S
1235J
2235T
1236J
2236U
1237J
2237V
1238J
2238W
1239J
2239X
1240J
2240Y
1241J
2241Z
1242J
2242a
1243J
2243b
1244J
2244c
1245J
2245d
1246K
2246L
1247K
2247M
1248K
2248N
1249K
2249O
1250K
2250P
1251K
2251Q
1252K
2252R
1253K
2253S
1254K
2254T
1255K
2255U
1256K
2256V
1257K
2257W
1258K
2258X
1259K
2259Y
1260K
2260Z
1261K
2261a
1262K
2262b
1263K
2263c
1264K
2264d
1265L
2265M
1266L
2266N
1267L
2267O
1268L
2268P
1269L
2269Q
1270L
2270R
1271L
2271S
1272L
2272T
1273L
2273U
1274L
2274V
1275L
2275W
1276L
2276X
1277L
2277Y
1278L
2278Z
1279L
2279a
1280L
2280b
1281L
2281c
1282L
2282d
1283M
2283N
1284M
2284O
1285M
2285P
1286M
2286Q
1287M
2287R
1288M
2288S
1289M
2289T
1290M
2290U
1291M
2291V
1292M
2292W
1293M
2293X
1294M
2294Y
1295M
2295Z
1296M
2296a
1297M
2297b
1298M
2298c
1299M
2299d
1300N
2300O
1301N
2301P
1302N
2302Q
1303N
2303R
1304N
2304S
1305N
2305T
1306N
2306U
1307N
2307V
1308N
2308W
1309N
2309X
1310N
2310Y
1311N
2311Z
1312N
2312a
1313N
2313b
1314N
2314c
1315N
2315d
1316O
2316P
1317O
2317Q
1318O
2318R
1319O
2319S
1320O
2320T
1321O
2321U
1322O
2322V
1323O
2323W
1324O
2324X
1325O
2325Y
1326O
2326Z
1327O
2327a
1328O
2328b
1329O
2329c
1330O
2330d
1331P
2331Q
1332P
2332R
1333P
2333S
1334P
2334T
1335P
2335U
1336P
2336V
1337P
2337W
1338P
2338X
1339P
2339Y
1340P
2340Z
1341P
2341a
1342P
2342b
1343P
2343c
1344P
2344d
1345Q
2345R
1346Q
2346S
1347Q
2347T
1348Q
2348U
1349Q
2349V
1350Q
2350W
1351Q
2351X
1352Q
2352Y
1353Q
2353Z
1354Q
2354a
1355Q
2355b
1356Q
2356c
1357Q
2357d
1358R
2358S
1359R
2359T
1360R
2360U
1361R
2361V
1362R
2362W
1363R
2363X
1364R
2364Y
1365R
2365Z
1366R
2366a
1367R
2367b
1368R
2368c
1369R
2369d
1370S
2370T
1371S
2371U
1372S
2372V
1373S
2373W
1374S
2374X
1375S
2375Y
1376S
2376Z
1377S
2377a
1378S
2378b
1379S
2379c
1380S
2380d
1381T
2381U
1382T
2382V
1383T
2383W
1384T
2384X
1385T
2385Y
1386T
2386Z
1387T
2387a
1388T
2388b
1389T
2389c
1390T
2390d
1391U
2391V
1392U
2392W
1393U
2393X
1394U
2394Y
1395U
2395Z
1396U
2396a
1397U
2397b
1398U
2398c
1399U
2399d
1400V
2400W
1401V
2401X
1402V
2402Y
1403V
2403Z
1404V
2404a
1405V
2405b
1406V
2406c
1407V
2407d
1408W
2408X
1409W
2409Y
1410W
2410Z
1411W
2411a
1412W
2412b
1413W
2413c
1414W
2414d
1415X
2415Y
1416X
2416Z
1417X
2417a
1418X
2418b
1419X
2419c
1420X
2420d
1421Y
2421Z
1422Y
2422a
1423Y
2423b
1424Y
2424c
1425Y
2425d
1426Z
2426a
1427Z
2427b
1428Z
2428c
1429Z
2429d
1430a
2430b
1431a
2431c
1432a
2432d
1433b
2433c
1434b
2434d
1435c
2435d

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 73 - 263 / Label seq-ID: 87 - 277

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18AA
28II
19AA
29JJ
110AA
210KK
111AA
211LL
112AA
212MM
113AA
213NN
114AA
214OO
115AA
215PP
116AA
216QQ
117AA
217RR
118AA
218SS
119AA
219TT
120AA
220UU
121AA
221VV
122AA
222WW
123AA
223XX
124AA
224YY
125AA
225ZZ
126AA
226aAA
127AA
227bBA
128AA
228cCA
129AA
229dDA
130BB
230CC
131BB
231DD
132BB
232EE
133BB
233FF
134BB
234GG
135BB
235HH
136BB
236II
137BB
237JJ
138BB
238KK
139BB
239LL
140BB
240MM
141BB
241NN
142BB
242OO
143BB
243PP
144BB
244QQ
145BB
245RR
146BB
246SS
147BB
247TT
148BB
248UU
149BB
249VV
150BB
250WW
151BB
251XX
152BB
252YY
153BB
253ZZ
154BB
254aAA
155BB
255bBA
156BB
256cCA
157BB
257dDA
158CC
258DD
159CC
259EE
160CC
260FF
161CC
261GG
162CC
262HH
163CC
263II
164CC
264JJ
165CC
265KK
166CC
266LL
167CC
267MM
168CC
268NN
169CC
269OO
170CC
270PP
171CC
271QQ
172CC
272RR
173CC
273SS
174CC
274TT
175CC
275UU
176CC
276VV
177CC
277WW
178CC
278XX
179CC
279YY
180CC
280ZZ
181CC
281aAA
182CC
282bBA
183CC
283cCA
184CC
284dDA
185DD
285EE
186DD
286FF
187DD
287GG
188DD
288HH
189DD
289II
190DD
290JJ
191DD
291KK
192DD
292LL
193DD
293MM
194DD
294NN
195DD
295OO
196DD
296PP
197DD
297QQ
198DD
298RR
199DD
299SS
1100DD
2100TT
1101DD
2101UU
1102DD
2102VV
1103DD
2103WW
1104DD
2104XX
1105DD
2105YY
1106DD
2106ZZ
1107DD
2107aAA
1108DD
2108bBA
1109DD
2109cCA
1110DD
2110dDA
1111EE
2111FF
1112EE
2112GG
1113EE
2113HH
1114EE
2114II
1115EE
2115JJ
1116EE
2116KK
1117EE
2117LL
1118EE
2118MM
1119EE
2119NN
1120EE
2120OO
1121EE
2121PP
1122EE
2122QQ
1123EE
2123RR
1124EE
2124SS
1125EE
2125TT
1126EE
2126UU
1127EE
2127VV
1128EE
2128WW
1129EE
2129XX
1130EE
2130YY
1131EE
2131ZZ
1132EE
2132aAA
1133EE
2133bBA
1134EE
2134cCA
1135EE
2135dDA
1136FF
2136GG
1137FF
2137HH
1138FF
2138II
1139FF
2139JJ
1140FF
2140KK
1141FF
2141LL
1142FF
2142MM
1143FF
2143NN
1144FF
2144OO
1145FF
2145PP
1146FF
2146QQ
1147FF
2147RR
1148FF
2148SS
1149FF
2149TT
1150FF
2150UU
1151FF
2151VV
1152FF
2152WW
1153FF
2153XX
1154FF
2154YY
1155FF
2155ZZ
1156FF
2156aAA
1157FF
2157bBA
1158FF
2158cCA
1159FF
2159dDA
1160GG
2160HH
1161GG
2161II
1162GG
2162JJ
1163GG
2163KK
1164GG
2164LL
1165GG
2165MM
1166GG
2166NN
1167GG
2167OO
1168GG
2168PP
1169GG
2169QQ
1170GG
2170RR
1171GG
2171SS
1172GG
2172TT
1173GG
2173UU
1174GG
2174VV
1175GG
2175WW
1176GG
2176XX
1177GG
2177YY
1178GG
2178ZZ
1179GG
2179aAA
1180GG
2180bBA
1181GG
2181cCA
1182GG
2182dDA
1183HH
2183II
1184HH
2184JJ
1185HH
2185KK
1186HH
2186LL
1187HH
2187MM
1188HH
2188NN
1189HH
2189OO
1190HH
2190PP
1191HH
2191QQ
1192HH
2192RR
1193HH
2193SS
1194HH
2194TT
1195HH
2195UU
1196HH
2196VV
1197HH
2197WW
1198HH
2198XX
1199HH
2199YY
1200HH
2200ZZ
1201HH
2201aAA
1202HH
2202bBA
1203HH
2203cCA
1204HH
2204dDA
1205II
2205JJ
1206II
2206KK
1207II
2207LL
1208II
2208MM
1209II
2209NN
1210II
2210OO
1211II
2211PP
1212II
2212QQ
1213II
2213RR
1214II
2214SS
1215II
2215TT
1216II
2216UU
1217II
2217VV
1218II
2218WW
1219II
2219XX
1220II
2220YY
1221II
2221ZZ
1222II
2222aAA
1223II
2223bBA
1224II
2224cCA
1225II
2225dDA
1226JJ
2226KK
1227JJ
2227LL
1228JJ
2228MM
1229JJ
2229NN
1230JJ
2230OO
1231JJ
2231PP
1232JJ
2232QQ
1233JJ
2233RR
1234JJ
2234SS
1235JJ
2235TT
1236JJ
2236UU
1237JJ
2237VV
1238JJ
2238WW
1239JJ
2239XX
1240JJ
2240YY
1241JJ
2241ZZ
1242JJ
2242aAA
1243JJ
2243bBA
1244JJ
2244cCA
1245JJ
2245dDA
1246KK
2246LL
1247KK
2247MM
1248KK
2248NN
1249KK
2249OO
1250KK
2250PP
1251KK
2251QQ
1252KK
2252RR
1253KK
2253SS
1254KK
2254TT
1255KK
2255UU
1256KK
2256VV
1257KK
2257WW
1258KK
2258XX
1259KK
2259YY
1260KK
2260ZZ
1261KK
2261aAA
1262KK
2262bBA
1263KK
2263cCA
1264KK
2264dDA
1265LL
2265MM
1266LL
2266NN
1267LL
2267OO
1268LL
2268PP
1269LL
2269QQ
1270LL
2270RR
1271LL
2271SS
1272LL
2272TT
1273LL
2273UU
1274LL
2274VV
1275LL
2275WW
1276LL
2276XX
1277LL
2277YY
1278LL
2278ZZ
1279LL
2279aAA
1280LL
2280bBA
1281LL
2281cCA
1282LL
2282dDA
1283MM
2283NN
1284MM
2284OO
1285MM
2285PP
1286MM
2286QQ
1287MM
2287RR
1288MM
2288SS
1289MM
2289TT
1290MM
2290UU
1291MM
2291VV
1292MM
2292WW
1293MM
2293XX
1294MM
2294YY
1295MM
2295ZZ
1296MM
2296aAA
1297MM
2297bBA
1298MM
2298cCA
1299MM
2299dDA
1300NN
2300OO
1301NN
2301PP
1302NN
2302QQ
1303NN
2303RR
1304NN
2304SS
1305NN
2305TT
1306NN
2306UU
1307NN
2307VV
1308NN
2308WW
1309NN
2309XX
1310NN
2310YY
1311NN
2311ZZ
1312NN
2312aAA
1313NN
2313bBA
1314NN
2314cCA
1315NN
2315dDA
1316OO
2316PP
1317OO
2317QQ
1318OO
2318RR
1319OO
2319SS
1320OO
2320TT
1321OO
2321UU
1322OO
2322VV
1323OO
2323WW
1324OO
2324XX
1325OO
2325YY
1326OO
2326ZZ
1327OO
2327aAA
1328OO
2328bBA
1329OO
2329cCA
1330OO
2330dDA
1331PP
2331QQ
1332PP
2332RR
1333PP
2333SS
1334PP
2334TT
1335PP
2335UU
1336PP
2336VV
1337PP
2337WW
1338PP
2338XX
1339PP
2339YY
1340PP
2340ZZ
1341PP
2341aAA
1342PP
2342bBA
1343PP
2343cCA
1344PP
2344dDA
1345QQ
2345RR
1346QQ
2346SS
1347QQ
2347TT
1348QQ
2348UU
1349QQ
2349VV
1350QQ
2350WW
1351QQ
2351XX
1352QQ
2352YY
1353QQ
2353ZZ
1354QQ
2354aAA
1355QQ
2355bBA
1356QQ
2356cCA
1357QQ
2357dDA
1358RR
2358SS
1359RR
2359TT
1360RR
2360UU
1361RR
2361VV
1362RR
2362WW
1363RR
2363XX
1364RR
2364YY
1365RR
2365ZZ
1366RR
2366aAA
1367RR
2367bBA
1368RR
2368cCA
1369RR
2369dDA
1370SS
2370TT
1371SS
2371UU
1372SS
2372VV
1373SS
2373WW
1374SS
2374XX
1375SS
2375YY
1376SS
2376ZZ
1377SS
2377aAA
1378SS
2378bBA
1379SS
2379cCA
1380SS
2380dDA
1381TT
2381UU
1382TT
2382VV
1383TT
2383WW
1384TT
2384XX
1385TT
2385YY
1386TT
2386ZZ
1387TT
2387aAA
1388TT
2388bBA
1389TT
2389cCA
1390TT
2390dDA
1391UU
2391VV
1392UU
2392WW
1393UU
2393XX
1394UU
2394YY
1395UU
2395ZZ
1396UU
2396aAA
1397UU
2397bBA
1398UU
2398cCA
1399UU
2399dDA
1400VV
2400WW
1401VV
2401XX
1402VV
2402YY
1403VV
2403ZZ
1404VV
2404aAA
1405VV
2405bBA
1406VV
2406cCA
1407VV
2407dDA
1408WW
2408XX
1409WW
2409YY
1410WW
2410ZZ
1411WW
2411aAA
1412WW
2412bBA
1413WW
2413cCA
1414WW
2414dDA
1415XX
2415YY
1416XX
2416ZZ
1417XX
2417aAA
1418XX
2418bBA
1419XX
2419cCA
1420XX
2420dDA
1421YY
2421ZZ
1422YY
2422aAA
1423YY
2423bBA
1424YY
2424cCA
1425YY
2425dDA
1426ZZ
2426aAA
1427ZZ
2427bBA
1428ZZ
2428cCA
1429ZZ
2429dDA
1430aAA
2430bBA
1431aAA
2431cCA
1432aAA
2432dDA
1433bBA
2433cCA
1434bBA
2434dDA
1435cCA
2435dDA

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435

-
Components

#1: Antibody ...
Immunoglobulin G-binding protein A,Coat protein / IgG-binding protein A / Staphylococcal protein A


Mass: 30543.213 Da / Num. of mol.: 30 / Fragment: UNP RESIDUES 158-211, RESIDUES 66-268
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF SPA (158-211), LINKER, AND COAT PROTEIN (66-268)
Source: (gene. exp.) Staphylococcus aureus (bacteria), (gene. exp.) Sesbania mosaic virus
Strain: NCTC 8325 / Gene: spa, SAOUHSC_00069 / Details (production host): pRSET A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta(DE3)pLysS / References: UniProt: P02976, UniProt: Q9EB06
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 15-20% PEG 4000, 5% Iso-propanol, 100 mM Sodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2012 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 169159 / % possible obs: 100 % / Redundancy: 5.1 % / Rsym value: 0.131 / Χ2: 1.008 / Net I/av σ(I): 12.13 / Net I/σ(I): 6.3 / Num. measured all: 863389
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3-3.054.90.732.584060.777100
3.05-3.114.90.58984370.767100
3.11-3.1750.47284490.794100
3.17-3.2350.41784430.786100
3.23-3.35.10.34984030.811100
3.3-3.385.10.31184590.811100
3.38-3.465.20.24584100.839100
3.46-3.565.20.19884560.849100
3.56-3.665.20.1784120.859100
3.66-3.785.20.13784820.893100
3.78-3.915.20.12584210.914100
3.91-4.075.20.11284320.93100
4.07-4.265.20.09984650.969100
4.26-4.485.20.07984571.032100
4.48-4.765.20.07184571.112100
4.76-5.135.20.07684801.202100
5.13-5.645.20.08884751.375100
5.64-6.465.10.0985081.575100
6.46-8.135.10.06585081.358100
8.13-5050.03685991.47499.7

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VAK
Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.922 / SU B: 12.79 / SU ML: 0.225 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 8494 5 %RANDOM
Rwork0.1791 160665 --
obs0.1802 160665 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.33 Å2 / Biso mean: 39.008 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42341 0 30 435 42806
Biso mean--5.59 15.97 -
Num. residues----5730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0243354
X-RAY DIFFRACTIONr_bond_other_d0.0080.0240062
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.94859502
X-RAY DIFFRACTIONr_angle_other_deg1.301392099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26755700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.44723.361354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41156343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.92315150
X-RAY DIFFRACTIONr_chiral_restr0.080.27231
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02148754
X-RAY DIFFRACTIONr_gen_planes_other0.0060.029352
X-RAY DIFFRACTIONr_mcbond_it3.0963.96622889
X-RAY DIFFRACTIONr_mcbond_other3.0963.96622888
X-RAY DIFFRACTIONr_mcangle_it4.8455.95228558
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A110260.05
12B110260.05
21A110160.05
22C110160.05
31A110950.04
32D110950.04
41A108320.04
42E108320.04
51A103940.06
52F103940.06
61A110840.05
62G110840.05
71A109650.04
72H109650.04
81A110880.04
82I110880.04
91A110310.05
92J110310.05
101A110960.04
102K110960.04
111A110590.04
112L110590.04
121A110080.04
122M110080.04
131A111010.04
132N111010.04
141A111470.03
142O111470.03
151A111300.04
152P111300.04
161A104650.06
162Q104650.06
171A107620.06
172R107620.06
181A107860.05
182S107860.05
191A110700.05
192T110700.05
201A110350.05
202U110350.05
211A110950.04
212V110950.04
221A110160.05
222W110160.05
231A109920.04
232X109920.04
241A110570.04
242Y110570.04
251A111500.02
252Z111500.02
261A110710.04
262a110710.04
271A110450.04
272b110450.04
281A110620.04
282c110620.04
291A110620.04
292d110620.04
301B110970.04
302C110970.04
311B111980.03
312D111980.03
321B109260.04
322E109260.04
331B103720.05
332F103720.05
341B111140.04
342G111140.04
351B109980.04
352H109980.04
361B111140.04
362I111140.04
371B111160.04
372J111160.04
381B110920.04
382K110920.04
391B112040.03
392L112040.03
401B110520.05
402M110520.05
411B111130.04
412N111130.04
421B111300.04
422O111300.04
431B111330.04
432P111330.04
441B104720.05
442Q104720.05
451B108250.06
452R108250.06
461B108550.05
462S108550.05
471B111230.05
472T111230.05
481B110170.04
482U110170.04
491B110600.05
492V110600.05
501B110750.05
502W110750.05
511B110570.04
512X110570.04
521B111040.04
522Y111040.04
531B110420.05
532Z110420.05
541B111740.04
542a111740.04
551B111780.03
552b111780.03
561B110770.04
562c110770.04
571B111310.04
572d111310.04
581C111270.03
582D111270.03
591C108520.05
592E108520.05
601C103460.06
602F103460.06
611C111640.03
612G111640.03
621C109660.04
622H109660.04
631C111680.03
632I111680.03
641C111560.03
642J111560.03
651C111430.02
652K111430.02
661C111370.03
662L111370.03
671C111100.05
672M111100.05
681C110380.04
682N110380.04
691C111170.04
692O111170.04
701C111230.03
702P111230.03
711C105290.05
712Q105290.05
721C108490.05
722R108490.05
731C108230.04
732S108230.04
741C110510.05
742T110510.05
751C109660.05
752U109660.05
761C110500.04
762V110500.04
771C111310.04
772W111310.04
781C111490.02
782X111490.02
791C110340.04
792Y110340.04
801C110320.04
802Z110320.04
811C110960.04
812a110960.04
821C111100.03
822b111100.03
831C111350.03
832c111350.03
841C110620.04
842d110620.04
851D109130.04
852E109130.04
861D103520.05
862F103520.05
871D111870.03
872G111870.03
881D110470.03
882H110470.03
891D111990.02
892I111990.02
901D111520.03
902J111520.03
911D111750.02
912K111750.02
921D112350.01
922L112350.01
931D110850.05
932M110850.05
941D111830.03
942N111830.03
951D111630.03
952O111630.03
961D111800.02
962P111800.02
971D104750.05
972Q104750.05
981D108270.05
982R108270.05
991D109020.03
992S109020.03
1001D111850.04
1002T111850.04
1011D110580.04
1012U110580.04
1021D111210.04
1022V111210.04
1031D111260.04
1032W111260.04
1041D111040.02
1042X111040.02
1051D111330.02
1052Y111330.02
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2002Z109920.03
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3951U110150.04
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3981U110080.04
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4021V109950.04
4022Y109950.04
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4211Y110720.03
4212Z110720.03
4221Y111360.02
4222a111360.02
4231Y111560.02
4232b111560.02
4241Y110180.04
4242c110180.04
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4261Z110850.03
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4272b110580.04
4281Z110280.04
4282c110280.04
4291Z110530.03
4292d110530.03
4301a111860.02
4302b111860.02
4311a110850.04
4312c110850.04
4321a111610.03
4322d111610.03
4331b111100.03
4332c111100.03
4341b111420.03
4342d111420.03
4351c111610.03
4352d111610.03
LS refinement shellResolution: 3.005→3.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 602 -
Rwork0.329 11432 -
all-12034 -
obs--96.29 %

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