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- PDB-4c3b: HRSV M2-1, P21 crystal form -

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Basic information

Entry
Database: PDB / ID: 4c3b
TitleHRSV M2-1, P21 crystal form
ComponentsMATRIX PROTEIN 2-1
KeywordsVIRAL PROTEIN / HRSV / M2-1
Function / homology
Function and homology information


: / regulation of viral transcription / viral transcription / virion component / transcription antitermination / host cell cytoplasm / host cell nucleus / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Pneumovirus matrix protein 2 (M2), zinc-binding domain / Pneumovirus matrix 2-1 / Pneumovirus matrix protein 2 (M2) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHUMAN RESPIRATORY SYNCYTIAL VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsTanner, S.J. / Ariza, A. / Richard, C.A. / Wu, W. / Trincao, J. / Hiscox, J.A. / Carroll, M.W. / Silman, N.J. / Eleouet, J.F. / Edwards, T.A. / Barr, J.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal Structure of the Essential Transcription Antiterminator M2-1 Protein of Human Respiratory Syncytial Virus and Implications of its Phosphorylation.
Authors: Tanner, S.J. / Ariza, A. / Richard, C. / Kyle, H.F. / Dods, R.L. / Blondot, M. / Wu, W. / Trincao, J. / Trinh, C.H. / Hiscox, J.A. / Carroll, M.W. / Silman, N.J. / Eleouet, J. / Edwards, T.A. / Barr, J.N.
History
DepositionAug 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MATRIX PROTEIN 2-1
B: MATRIX PROTEIN 2-1
C: MATRIX PROTEIN 2-1
D: MATRIX PROTEIN 2-1
E: MATRIX PROTEIN 2-1
F: MATRIX PROTEIN 2-1
G: MATRIX PROTEIN 2-1
H: MATRIX PROTEIN 2-1
I: MATRIX PROTEIN 2-1
J: MATRIX PROTEIN 2-1
K: MATRIX PROTEIN 2-1
L: MATRIX PROTEIN 2-1
M: MATRIX PROTEIN 2-1
N: MATRIX PROTEIN 2-1
O: MATRIX PROTEIN 2-1
P: MATRIX PROTEIN 2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,67532
Polymers361,62816
Non-polymers1,04716
Water3,207178
1
I: MATRIX PROTEIN 2-1
J: MATRIX PROTEIN 2-1
K: MATRIX PROTEIN 2-1
L: MATRIX PROTEIN 2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6698
Polymers90,4074
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13630 Å2
ΔGint-43.7 kcal/mol
Surface area32230 Å2
MethodPISA
2
M: MATRIX PROTEIN 2-1
N: MATRIX PROTEIN 2-1
O: MATRIX PROTEIN 2-1
P: MATRIX PROTEIN 2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6698
Polymers90,4074
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13620 Å2
ΔGint-43.6 kcal/mol
Surface area31940 Å2
MethodPISA
3
A: MATRIX PROTEIN 2-1
B: MATRIX PROTEIN 2-1
C: MATRIX PROTEIN 2-1
D: MATRIX PROTEIN 2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6698
Polymers90,4074
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-43.4 kcal/mol
Surface area35200 Å2
MethodPISA
4
E: MATRIX PROTEIN 2-1
F: MATRIX PROTEIN 2-1
G: MATRIX PROTEIN 2-1
H: MATRIX PROTEIN 2-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6698
Polymers90,4074
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14060 Å2
ΔGint-42.5 kcal/mol
Surface area35060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.853, 141.616, 141.694
Angle α, β, γ (deg.)90.00, 96.14, 90.00
Int Tables number4
Space group name H-MP1211
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
116B
216C
117B
217D
118B
218E
119B
219F
120B
220G
121B
221H
122B
222I
123B
223J
124B
224K
125B
225L
126B
226M
127B
227N
128B
228O
129B
229P
130C
230D
131C
231E
132C
232F
133C
233G
134C
234H
135C
235I
136C
236J
137C
237K
138C
238L
139C
239M
140C
240N
141C
241O
142C
242P
143D
243E
144D
244F
145D
245G
146D
246H
147D
247I
148D
248J
149D
249K
150D
250L
151D
251M
152D
252N
153D
253O
154D
254P
155E
255F
156E
256G
157E
257H
158E
258I
159E
259J
160E
260K
161E
261L
162E
262M
163E
263N
164E
264O
165E
265P
166F
266G
167F
267H
168F
268I
169F
269J
170F
270K
171F
271L
172F
272M
173F
273N
174F
274O
175F
275P
176G
276H
177G
277I
178G
278J
179G
279K
180G
280L
181G
281M
182G
282N
183G
283O
184G
284P
185H
285I
186H
286J
187H
287K
188H
288L
189H
289M
190H
290N
191H
291O
192H
292P
193I
293J
194I
294K
195I
295L
196I
296M
197I
297N
198I
298O
199I
299P
1100J
2100K
1101J
2101L
1102J
2102M
1103J
2103N
1104J
2104O
1105J
2105P
1106K
2106L
1107K
2107M
1108K
2108N
1109K
2109O
1110K
2110P
1111L
2111M
1112L
2112N
1113L
2113O
1114L
2114P
1115M
2115N
1116M
2116O
1117M
2117P
1118N
2118O
1119N
2119P
1120O
2120P

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROASNASNAA-3 - 1742 - 179
21PROPROASNASNBB-3 - 1742 - 179
12PROPROASNASNAA-3 - 1742 - 179
22PROPROASNASNCC-3 - 1742 - 179
13PROPROASNASNAA-3 - 1742 - 179
23PROPROASNASNDD-3 - 1742 - 179
14PROPROASNASNAA-3 - 1742 - 179
24PROPROASNASNEE-3 - 1742 - 179
15PROPROASNASNAA-3 - 1742 - 179
25PROPROASNASNFF-3 - 1742 - 179
16PROPROASNASNAA-3 - 1742 - 179
26PROPROASNASNGG-3 - 1742 - 179
17PROPROASNASNAA-3 - 1742 - 179
27PROPROASNASNHH-3 - 1742 - 179
18ARGARGILEILEAA3 - 1738 - 178
28ARGARGILEILEII3 - 1738 - 178
19ARGARGILEILEAA3 - 1738 - 178
29ARGARGILEILEJJ3 - 1738 - 178
110ARGARGASNASNAA4 - 1749 - 179
210ARGARGASNASNKK4 - 1749 - 179
111ARGARGILEILEAA4 - 1739 - 178
211ARGARGILEILELL4 - 1739 - 178
112ARGARGILEILEAA4 - 1739 - 178
212ARGARGILEILEMM4 - 1739 - 178
113ARGARGILEILEAA4 - 1739 - 178
213ARGARGILEILENN4 - 1739 - 178
114ARGARGASNASNAA3 - 1748 - 179
214ARGARGASNASNOO3 - 1748 - 179
115ARGARGILEILEAA4 - 1739 - 178
215ARGARGILEILEPP4 - 1739 - 178
116PROPROASNASNBB-3 - 1742 - 179
216PROPROASNASNCC-3 - 1742 - 179
117PROPROASNASNBB-3 - 1742 - 179
217PROPROASNASNDD-3 - 1742 - 179
118PROPROASNASNBB-3 - 1742 - 179
218PROPROASNASNEE-3 - 1742 - 179
119PROPROASNASNBB-3 - 1742 - 179
219PROPROASNASNFF-3 - 1742 - 179
120PROPROASNASNBB-3 - 1742 - 179
220PROPROASNASNGG-3 - 1742 - 179
121PROPROASNASNBB-3 - 1742 - 179
221PROPROASNASNHH-3 - 1742 - 179
122ARGARGILEILEBB3 - 1738 - 178
222ARGARGILEILEII3 - 1738 - 178
123ARGARGILEILEBB3 - 1738 - 178
223ARGARGILEILEJJ3 - 1738 - 178
124ARGARGASNASNBB4 - 1749 - 179
224ARGARGASNASNKK4 - 1749 - 179
125ARGARGILEILEBB4 - 1739 - 178
225ARGARGILEILELL4 - 1739 - 178
126ARGARGILEILEBB4 - 1739 - 178
226ARGARGILEILEMM4 - 1739 - 178
127ARGARGILEILEBB4 - 1739 - 178
227ARGARGILEILENN4 - 1739 - 178
128ARGARGASNASNBB3 - 1748 - 179
228ARGARGASNASNOO3 - 1748 - 179
129ARGARGILEILEBB4 - 1739 - 178
229ARGARGILEILEPP4 - 1739 - 178
130PROPROASNASNCC-3 - 1742 - 179
230PROPROASNASNDD-3 - 1742 - 179
131PROPROASNASNCC-3 - 1742 - 179
231PROPROASNASNEE-3 - 1742 - 179
132PROPROASNASNCC-3 - 1742 - 179
232PROPROASNASNFF-3 - 1742 - 179
133PROPROASNASNCC-3 - 1742 - 179
233PROPROASNASNGG-3 - 1742 - 179
134PROPROASNASNCC-3 - 1742 - 179
234PROPROASNASNHH-3 - 1742 - 179
135ARGARGASNASNCC3 - 1748 - 179
235ARGARGASNASNII3 - 1748 - 179
136ARGARGASNASNCC3 - 1748 - 179
236ARGARGASNASNJJ3 - 1748 - 179
137ARGARGILEILECC4 - 1739 - 178
237ARGARGILEILEKK4 - 1739 - 178
138ARGARGASNASNCC4 - 1749 - 179
238ARGARGASNASNLL4 - 1749 - 179
139ARGARGASNASNCC4 - 1749 - 179
239ARGARGASNASNMM4 - 1749 - 179
140ARGARGASNASNCC4 - 1749 - 179
240ARGARGASNASNNN4 - 1749 - 179
141ARGARGILEILECC3 - 1738 - 178
241ARGARGILEILEOO3 - 1738 - 178
142ARGARGASNASNCC4 - 1749 - 179
242ARGARGASNASNPP4 - 1749 - 179
143PROPROASNASNDD-3 - 1742 - 179
243PROPROASNASNEE-3 - 1742 - 179
144PROPROASNASNDD-3 - 1742 - 179
244PROPROASNASNFF-3 - 1742 - 179
145PROPROASNASNDD-3 - 1742 - 179
245PROPROASNASNGG-3 - 1742 - 179
146PROPROASNASNDD-3 - 1742 - 179
246PROPROASNASNHH-3 - 1742 - 179
147ARGARGASNASNDD3 - 1748 - 179
247ARGARGASNASNII3 - 1748 - 179
148ARGARGASNASNDD3 - 1748 - 179
248ARGARGASNASNJJ3 - 1748 - 179
149ARGARGILEILEDD4 - 1739 - 178
249ARGARGILEILEKK4 - 1739 - 178
150ARGARGASNASNDD4 - 1749 - 179
250ARGARGASNASNLL4 - 1749 - 179
151ARGARGILEILEDD4 - 1739 - 178
251ARGARGILEILEMM4 - 1739 - 178
152ARGARGASNASNDD4 - 1749 - 179
252ARGARGASNASNNN4 - 1749 - 179
153ARGARGILEILEDD3 - 1738 - 178
253ARGARGILEILEOO3 - 1738 - 178
154ARGARGASNASNDD4 - 1749 - 179
254ARGARGASNASNPP4 - 1749 - 179
155PROPROASNASNEE-3 - 1742 - 179
255PROPROASNASNFF-3 - 1742 - 179
156PROPROASNASNEE-3 - 1742 - 179
256PROPROASNASNGG-3 - 1742 - 179
157PROPROASNASNEE-3 - 1742 - 179
257PROPROASNASNHH-3 - 1742 - 179
158ARGARGASNASNEE3 - 1748 - 179
258ARGARGASNASNII3 - 1748 - 179
159ARGARGASNASNEE3 - 1748 - 179
259ARGARGASNASNJJ3 - 1748 - 179
160ARGARGILEILEEE4 - 1739 - 178
260ARGARGILEILEKK4 - 1739 - 178
161ARGARGASNASNEE4 - 1749 - 179
261ARGARGASNASNLL4 - 1749 - 179
162ARGARGILEILEEE4 - 1739 - 178
262ARGARGILEILEMM4 - 1739 - 178
163ARGARGASNASNEE4 - 1749 - 179
263ARGARGASNASNNN4 - 1749 - 179
164ARGARGILEILEEE3 - 1738 - 178
264ARGARGILEILEOO3 - 1738 - 178
165ARGARGASNASNEE4 - 1749 - 179
265ARGARGASNASNPP4 - 1749 - 179
166PROPROASNASNFF-3 - 1742 - 179
266PROPROASNASNGG-3 - 1742 - 179
167PROPROASNASNFF-3 - 1742 - 179
267PROPROASNASNHH-3 - 1742 - 179
168ARGARGASNASNFF3 - 1748 - 179
268ARGARGASNASNII3 - 1748 - 179
169ARGARGASNASNFF3 - 1748 - 179
269ARGARGASNASNJJ3 - 1748 - 179
170ARGARGILEILEFF4 - 1739 - 178
270ARGARGILEILEKK4 - 1739 - 178
171ARGARGASNASNFF4 - 1749 - 179
271ARGARGASNASNLL4 - 1749 - 179
172ARGARGASNASNFF4 - 1749 - 179
272ARGARGASNASNMM4 - 1749 - 179
173ARGARGASNASNFF4 - 1749 - 179
273ARGARGASNASNNN4 - 1749 - 179
174ARGARGILEILEFF3 - 1738 - 178
274ARGARGILEILEOO3 - 1738 - 178
175ARGARGASNASNFF4 - 1749 - 179
275ARGARGASNASNPP4 - 1749 - 179
176PROPROASNASNGG-3 - 1742 - 179
276PROPROASNASNHH-3 - 1742 - 179
177ARGARGILEILEGG3 - 1738 - 178
277ARGARGILEILEII3 - 1738 - 178
178ARGARGILEILEGG3 - 1738 - 178
278ARGARGILEILEJJ3 - 1738 - 178
179ARGARGASNASNGG4 - 1749 - 179
279ARGARGASNASNKK4 - 1749 - 179
180ARGARGILEILEGG4 - 1739 - 178
280ARGARGILEILELL4 - 1739 - 178
181ARGARGILEILEGG4 - 1739 - 178
281ARGARGILEILEMM4 - 1739 - 178
182ARGARGILEILEGG4 - 1739 - 178
282ARGARGILEILENN4 - 1739 - 178
183ARGARGASNASNGG3 - 1748 - 179
283ARGARGASNASNOO3 - 1748 - 179
184ARGARGILEILEGG4 - 1739 - 178
284ARGARGILEILEPP4 - 1739 - 178
185ARGARGASNASNHH3 - 1748 - 179
285ARGARGASNASNII3 - 1748 - 179
186ARGARGASNASNHH3 - 1748 - 179
286ARGARGASNASNJJ3 - 1748 - 179
187ARGARGASNASNHH4 - 1749 - 179
287ARGARGASNASNKK4 - 1749 - 179
188ARGARGASNASNHH4 - 1749 - 179
288ARGARGASNASNLL4 - 1749 - 179
189ARGARGILEILEHH4 - 1739 - 178
289ARGARGILEILEMM4 - 1739 - 178
190ARGARGASNASNHH4 - 1749 - 179
290ARGARGASNASNNN4 - 1749 - 179
191ARGARGILEILEHH3 - 1738 - 178
291ARGARGILEILEOO3 - 1738 - 178
192ARGARGASNASNHH4 - 1749 - 179
292ARGARGASNASNPP4 - 1749 - 179
193ARGARGASNASNII3 - 1748 - 179
293ARGARGASNASNJJ3 - 1748 - 179
194ARGARGASNASNII4 - 1749 - 179
294ARGARGASNASNKK4 - 1749 - 179
195ARGARGASNASNII4 - 1749 - 179
295ARGARGASNASNLL4 - 1749 - 179
196ARGARGASNASNII4 - 1749 - 179
296ARGARGASNASNMM4 - 1749 - 179
197ARGARGILEILEII4 - 1739 - 178
297ARGARGILEILENN4 - 1739 - 178
198ARGARGASNASNII3 - 1748 - 179
298ARGARGASNASNOO3 - 1748 - 179
199ARGARGASNASNII4 - 1749 - 179
299ARGARGASNASNPP4 - 1749 - 179
1100ARGARGASNASNJJ4 - 1749 - 179
2100ARGARGASNASNKK4 - 1749 - 179
1101ARGARGILEILEJJ4 - 1739 - 178
2101ARGARGILEILELL4 - 1739 - 178
1102ARGARGASNASNJJ4 - 1749 - 179
2102ARGARGASNASNMM4 - 1749 - 179
1103ARGARGASNASNJJ4 - 1749 - 179
2103ARGARGASNASNNN4 - 1749 - 179
1104ARGARGASNASNJJ3 - 1748 - 179
2104ARGARGASNASNOO3 - 1748 - 179
1105ARGARGILEILEJJ4 - 1739 - 178
2105ARGARGILEILEPP4 - 1739 - 178
1106ARGARGASNASNKK4 - 1749 - 179
2106ARGARGASNASNLL4 - 1749 - 179
1107ARGARGASNASNKK4 - 1749 - 179
2107ARGARGASNASNMM4 - 1749 - 179
1108ARGARGASNASNKK4 - 1749 - 179
2108ARGARGASNASNNN4 - 1749 - 179
1109ARGARGASNASNKK4 - 1749 - 179
2109ARGARGASNASNOO4 - 1749 - 179
1110ARGARGASNASNKK4 - 1749 - 179
2110ARGARGASNASNPP4 - 1749 - 179
1111ARGARGASNASNLL4 - 1749 - 179
2111ARGARGASNASNMM4 - 1749 - 179
1112ARGARGASNASNLL4 - 1749 - 179
2112ARGARGASNASNNN4 - 1749 - 179
1113ARGARGASNASNLL4 - 1749 - 179
2113ARGARGASNASNOO4 - 1749 - 179
1114ARGARGASNASNLL4 - 1749 - 179
2114ARGARGASNASNPP4 - 1749 - 179
1115ARGARGASNASNMM4 - 1749 - 179
2115ARGARGASNASNNN4 - 1749 - 179
1116ARGARGASNASNMM4 - 1749 - 179
2116ARGARGASNASNOO4 - 1749 - 179
1117ARGARGASNASNMM4 - 1749 - 179
2117ARGARGASNASNPP4 - 1749 - 179
1118ARGARGASNASNNN4 - 1749 - 179
2118ARGARGASNASNOO4 - 1749 - 179
1119ARGARGASNASNNN4 - 1749 - 179
2119ARGARGASNASNPP4 - 1749 - 179
1120ARGARGASNASNOO4 - 1749 - 179
2120ARGARGASNASNPP4 - 1749 - 179

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

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Components

#1: Protein
MATRIX PROTEIN 2-1 / HRSV M2-1 / ENVELOPE-ASSOCIATED 22 KDA PROTEIN


Mass: 22601.779 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN RESPIRATORY SYNCYTIAL VIRUS / Strain: A2 / Plasmid: PGEX-6P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: P04545
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE INITIAL AMINO ACIDS ARE THE REMNANT OF REMOVING AN N- TERMINAL GST TAG

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Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.52 % / Description: NONE
Crystal growpH: 10 / Details: 30 % (V/V) PEG 400, 0.1 M CAPS PH 10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.2819
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2819 Å / Relative weight: 1
ReflectionResolution: 2.95→140.88 Å / Num. obs: 75535 / % possible obs: 99.5 % / Redundancy: 15 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 14.4
Reflection shellResolution: 2.95→3.01 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 2.3 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→140.88 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 18.336 / SU ML: 0.33 / Cross valid method: THROUGHOUT / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25458 3797 5 %RANDOM
Rwork0.20538 ---
obs0.20787 71711 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.598 Å2
Baniso -1Baniso -2Baniso -3
1-7.85 Å20 Å21.51 Å2
2---3.74 Å20 Å2
3----4.17 Å2
Refinement stepCycle: LAST / Resolution: 2.95→140.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21486 0 16 178 21680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01921825
X-RAY DIFFRACTIONr_bond_other_d0.0070.0221813
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.96529346
X-RAY DIFFRACTIONr_angle_other_deg1.097350161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96252632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85724.0561006
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.294154333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.30215171
X-RAY DIFFRACTIONr_chiral_restr0.0840.23361
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0224100
X-RAY DIFFRACTIONr_gen_planes_other0.0070.024963
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.4896.51210612
X-RAY DIFFRACTIONr_mcbond_other6.4876.51210611
X-RAY DIFFRACTIONr_mcangle_it9.9879.73813213
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.0457.2311213
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A100290.02
12B100290.02
21A102120.02
22C102120.02
31A102340.02
32D102340.02
41A102330.02
42E102330.02
51A101970.02
52F101970.02
61A101700.02
62G101700.02
71A102170.02
72H102170.02
81A97310.02
82I97310.02
91A99760.01
92J99760.01
101A99540.01
102K99540.01
111A99090.02
112L99090.02
121A99170.02
122M99170.02
131A96370.03
132N96370.03
141A100130.01
142O100130.01
151A99060.02
152P99060.02
161B101010.03
162C101010.03
171B101320.02
172D101320.02
181B101370.02
182E101370.02
191B100880.03
192F100880.03
201B100640.02
202G100640.02
211B101310.02
212H101310.02
221B97790.01
222I97790.01
231B98650.01
232J98650.01
241B97610.03
242K97610.03
251B98060
252L98060
261B98070
262M98070
271B97150.02
272N97150.02
281B99000.02
282O99000.02
291B97350.02
292P97350.02
301C107810.03
302D107810.03
311C107860.03
312E107860.03
321C110900.01
322F110900.01
331C101730.01
332G101730.01
341C108000.03
342H108000.03
351C97920.01
352I97920.01
361C101050.03
362J101050.03
371C104580.02
372K104580.02
381C100550.02
382L100550.02
391C101020.02
392M101020.02
401C97150.03
402N97150.03
411C105450.04
412O105450.04
421C100360.01
422P100360.01
431D108190.01
432E108190.01
441D107700.03
442F107700.03
451D101970
452G101970
461D104490.04
462H104490.04
471D97910.01
472I97910.01
481D101350.01
482J101350.01
491D104040.02
492K104040.02
501D100930
502L100930
511D101060
512M101060
521D97470.02
522N97470.02
531D105440.01
532O105440.01
541D100620
542P100620
551E107680.03
552F107680.03
561E101970.01
562G101970.01
571E104510.04
572H104510.04
581E97940.01
582I97940.01
591E101420.01
592J101420.01
601E104140.02
602K104140.02
611E100920
612L100920
621E101030
622M101030
631E97510.02
632N97510.02
641E105560.01
642O105560.01
651E100580.01
652P100580.01
661F101670.02
662G101670.02
671F107860.04
672H107860.04
681F97800.02
682I97800.02
691F100830.03
692J100830.03
701F104300.02
702K104300.02
711F100410.03
712L100410.03
721F100850.03
722M100850.03
731F97120.03
732N97120.03
741F105240.04
742O105240.04
751F100240.02
752P100240.02
761G101770.01
762H101770.01
771G97650.01
772I97650.01
781G99240.01
782J99240.01
791G98960.01
792K98960.01
801G98700
802L98700
811G98760
812M98760
821G96340.03
822N96340.03
831G99620.01
832O99620.01
841G98670
842P98670
851H97940.01
852I97940.01
861H101040.02
862J101040.02
871H102200.03
872K102200.03
881H100550.01
882L100550.01
891H100320.01
892M100320.01
901H97440.02
902N97440.02
911H101690.04
912O101690.04
921H99760.01
922P99760.01
931I97990.02
932J97990.02
941I97260.02
942K97260.02
951I97350.01
952L97350.01
961I97390.01
962M97390.01
971I96550.03
972N96550.03
981I98050.02
982O98050.02
991I97340.01
992P97340.01
1001J100130.01
1002K100130.01
1011J100430.01
1012L100430.01
1021J100760.01
1022M100760.01
1031J97590.01
1032N97590.01
1041J101660
1042O101660
1051J99670.02
1052P99670.02
1061K100280.02
1062L100280.02
1071K100700.01
1072M100700.01
1081K97030.03
1082N97030.03
1091K104580.02
1092O104580.02
1101K100650.01
1102P100650.01
1111L101050
1112M101050
1121L97680.02
1122N97680.02
1131L100870.01
1132O100870.01
1141L100410.01
1142P100410.01
1151M97650.02
1152N97650.02
1161M101300.01
1162O101300.01
1171M100760
1172P100760
1181N97600.01
1182O97600.01
1191N96930.03
1192P96930.03
1201O100520.01
1202P100520.01
LS refinement shellResolution: 2.95→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 254 -
Rwork0.319 5192 -
obs--98.21 %

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