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- PDB-3aq0: Ligand-bound form of Arabidopsis medium/long-chain length prenyl ... -

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Basic information

Entry
Database: PDB / ID: 3aq0
TitleLigand-bound form of Arabidopsis medium/long-chain length prenyl pyrophosphate synthase (surface polar residue mutant)
ComponentsGeranyl diphosphate synthase
KeywordsTRANSFERASE / prenyltransferase / All alpha-helices fold / chroloplast / isoprenoid biosynthetic process
Function / homology
Function and homology information


all-trans-nonaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific] / all-trans-nonaprenyl-diphosphate synthase (geranylgeranyl-diphosphate specific) activity / ubiquinone biosynthetic process / embryo development ending in seed dormancy / prenyltransferase activity / plastid / isoprenoid biosynthetic process / chloroplast / mitochondrion / metal ion binding
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FARNESYL DIPHOSPHATE / Chem-ISY / DI(HYDROXYETHYL)ETHER / PYROPHOSPHATE / Solanesyl diphosphate synthase 3, chloroplastic/mitochondrial / Solanesyl diphosphate synthase 3, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsHsieh, F.-L. / Chang, T.-H. / Ko, T.-P. / Wang, A.H.-J.
CitationJournal: Plant Physiol. / Year: 2011
Title: Structure and mechanism of an Arabidopsis medium/long-chain-length prenyl pyrophosphate synthase
Authors: Hsieh, F.-L. / Chang, T.-H. / Ko, T.-P. / Wang, A.H.-J.
History
DepositionOct 24, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_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_ref_seq_dif.details / _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: Geranyl diphosphate synthase
B: Geranyl diphosphate synthase
C: Geranyl diphosphate synthase
D: Geranyl diphosphate synthase
E: Geranyl diphosphate synthase
F: Geranyl diphosphate synthase
G: Geranyl diphosphate synthase
H: Geranyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,04732
Polymers302,7558
Non-polymers4,29324
Water12,520695
1
A: Geranyl diphosphate synthase
B: Geranyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0489
Polymers75,6892
Non-polymers1,3607
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-26 kcal/mol
Surface area30260 Å2
MethodPISA
2
C: Geranyl diphosphate synthase
D: Geranyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5828
Polymers75,6892
Non-polymers8936
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-28 kcal/mol
Surface area30420 Å2
MethodPISA
3
E: Geranyl diphosphate synthase
F: Geranyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4767
Polymers75,6892
Non-polymers7875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-27 kcal/mol
Surface area29990 Å2
MethodPISA
4
G: Geranyl diphosphate synthase
H: Geranyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9428
Polymers75,6892
Non-polymers1,2536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-27 kcal/mol
Surface area30000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.961, 115.961, 385.874
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21H
12E
22C
13B
23G
14D
24F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROLYSLYS4AA10 - 3510 - 35
211PROPROLYSLYS4HH10 - 3510 - 35
121LEULEULEULEU3AA36 - 6536 - 65
221LEULEULEULEU3HH36 - 6536 - 65
131VALVALHISHIS2AA87 - 10687 - 106
231VALVALHISHIS2HH87 - 10687 - 106
141ASPASPGLYGLY4AA107 - 120107 - 120
241ASPASPGLYGLY4HH107 - 120107 - 120
151SERSERTHRTHR2AA121 - 170121 - 170
251SERSERTHRTHR2HH121 - 170121 - 170
161METMETTYRTYR4AA171 - 181171 - 181
261METMETTYRTYR4HH171 - 181171 - 181
171SERSERVALVAL2AA182 - 207182 - 207
271SERSERVALVAL2HH182 - 207182 - 207
181LEULEULEULEU4AA208 - 218208 - 218
281LEULEULEULEU4HH208 - 218208 - 218
191ALAALAPHEPHE2AA219 - 239219 - 239
291ALAALAPHEPHE2HH219 - 239219 - 239
1101THRTHRGLYGLY4AA240 - 257240 - 257
2101THRTHRGLYGLY4HH240 - 257240 - 257
1111VALVALPROPRO3AA258 - 271258 - 271
2111VALVALPROPRO3HH258 - 271258 - 271
1121GLNGLNARGARG4AA272 - 331272 - 331
2121GLNGLNARGARG4HH272 - 331272 - 331
1131SERSERTHRTHR3AA332 - 345332 - 345
2131SERSERTHRTHR3HH332 - 345332 - 345
112PHEPHELEULEU4EE11 - 6511 - 65
212PHEPHELEULEU4CC11 - 6511 - 65
122ARGARGHISHIS2EE86 - 10086 - 100
222ARGARGHISHIS2CC86 - 10086 - 100
132VALVALHISHIS2EE101 - 106101 - 106
232VALVALHISHIS2CC101 - 106101 - 106
142ASPASPLYSLYS4EE107 - 129107 - 129
242ASPASPLYSLYS4CC107 - 129107 - 129
152METMETMETMET2EE130 - 171130 - 171
252METMETMETMET2CC130 - 171130 - 171
162GLUGLUSERSER4EE172 - 182172 - 182
262GLUGLUSERSER4CC172 - 182172 - 182
172METMETTHRTHR2EE183 - 209183 - 209
272METMETTHRTHR2CC183 - 209183 - 209
182GLYGLYALAALA4EE210 - 219210 - 219
282GLYGLYALAALA4CC210 - 219210 - 219
192PHEPHELEULEU2EE220 - 237220 - 237
292PHEPHELEULEU2CC220 - 237220 - 237
1102ASPASPVALVAL4EE238 - 258238 - 258
2102ASPASPVALVAL4CC238 - 258238 - 258
1112ILEILEPHEPHE3EE259 - 265259 - 265
2112ILEILEPHEPHE3CC259 - 265259 - 265
1122ALAALAILEILE4EE266 - 300266 - 300
2122ALAALAILEILE4CC266 - 300266 - 300
1132GLNGLNILEILE3EE301 - 344301 - 344
2132GLNGLNILEILE3CC301 - 344301 - 344
113PROPROPROPRO5BB10 - 3410 - 34
213PROPROPROPRO5GG10 - 3410 - 34
123LYSLYSTYRTYR4BB35 - 4235 - 42
223LYSLYSTYRTYR4GG35 - 4235 - 42
133PHEPHELYSLYS5BB43 - 5143 - 51
233PHEPHELYSLYS5GG43 - 5143 - 51
143GLNGLNASPASP2BB52 - 6652 - 66
243GLNGLNASPASP2GG52 - 6652 - 66
153LEULEUHISHIS3BB85 - 10685 - 106
253LEULEUHISHIS3GG85 - 10685 - 106
163METMETTYRTYR4BB130 - 181130 - 181
263METMETTYRTYR4GG130 - 181130 - 181
173SERSERALAALA3BB182 - 219182 - 219
273SERSERALAALA3GG182 - 219182 - 219
183PHEPHEILEILE2BB220 - 236220 - 236
283PHEPHEILEILE2GG220 - 236220 - 236
193LEULEUVALVAL4BB237 - 329237 - 329
293LEULEUVALVAL4GG237 - 329237 - 329
1103LYSLYSTHRTHR3BB330 - 345330 - 345
2103LYSLYSTHRTHR3GG330 - 345330 - 345
114PROPROGLUGLU5DD10 - 4110 - 41
214PROPROGLUGLU5FF10 - 4110 - 41
124ARGARGLEULEU4DD54 - 6554 - 65
224ARGARGLEULEU4FF54 - 6554 - 65
134LEULEULEULEU4DD85 - 11085 - 110
234LEULEULEULEU4FF85 - 11085 - 110
144METMETTHRTHR4DD130 - 170130 - 170
244METMETTHRTHR4FF130 - 170130 - 170
154METMETARGARG5DD171 - 180171 - 180
254METMETARGARG5FF171 - 180171 - 180
164TYRTYRALAALA4DD181 - 219181 - 219
264TYRTYRALAALA4FF181 - 219181 - 219
174PHEPHEPHEPHE2DD220 - 239220 - 239
274PHEPHEPHEPHE2FF220 - 239220 - 239
184THRTHRPROPRO4DD240 - 262240 - 262
284THRTHRPROPRO4FF240 - 262240 - 262
194ILEILELEULEU5DD263 - 291263 - 291
294ILEILELEULEU5FF263 - 291263 - 291
1104GLUGLUPROPRO4DD292 - 322292 - 322
2104GLUGLUPROPRO4FF292 - 322292 - 322
1114GLUGLUTHRTHR3DD323 - 345323 - 345
2114GLUGLUTHRTHR3FF323 - 345323 - 345

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Geranyl diphosphate synthase


Mass: 37844.316 Da / Num. of mol.: 8 / Fragment: residues in UNP 76-422 / Mutation: E178A,Q179A,E281A,K282A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AtNPPPS, gpps / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9FT89, UniProt: Q5HZ00*PLUS, heptaprenyl diphosphate synthase

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Non-polymers , 6 types, 719 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FPP / FARNESYL DIPHOSPHATE / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H28O7P2
#4: Chemical ChemComp-ISY / 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid / Isopentyl S-Thiolodiphosphate


Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O6P2S
#5: Chemical
ChemComp-PPV / PYROPHOSPHATE / Pyrophosphate


Mass: 177.975 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H4O7P2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6
Details: 18%(w/v) PEG3350, 0.17M Sodium thiocyanate, pH 6.0, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2009
RadiationMonochromator: Horizontally Focusing Single Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.944
11-H-K, K, -L20.056
ReflectionResolution: 2.65→30 Å / Num. obs: 83662 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 78.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 28.3
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.1 / Num. unique all: 21336 / % possible all: 97.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3APZ

3apz


Resolution: 2.65→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2721 / WRfactor Rwork: 0.2224 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7657 / SU B: 25.823 / SU ML: 0.245 / SU Rfree: 0.0799 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.274 4284 5.1 %RANDOM
Rwork0.222 ---
obs0.2247 83456 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 132.01 Å2 / Biso mean: 77.543 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--24.33 Å20 Å20 Å2
2---24.33 Å20 Å2
3---48.67 Å2
Refinement stepCycle: LAST / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19483 0 248 695 20426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02219926
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.99226939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19252529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94223.812821
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.18153547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.76915158
X-RAY DIFFRACTIONr_chiral_restr0.0940.23268
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214462
X-RAY DIFFRACTIONr_mcbond_it0.4591.512645
X-RAY DIFFRACTIONr_mcangle_it0.907220238
X-RAY DIFFRACTIONr_scbond_it1.44237281
X-RAY DIFFRACTIONr_scangle_it2.5214.56701
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A700TIGHT POSITIONAL0.030.05
1A1467MEDIUM POSITIONAL0.040.5
1A227LOOSE POSITIONAL0.055
1A700TIGHT THERMAL0.060.5
1A1467MEDIUM THERMAL0.062
1A227LOOSE THERMAL0.0710
2E636TIGHT POSITIONAL0.030.05
2E1562MEDIUM POSITIONAL0.070.5
2E193LOOSE POSITIONAL0.055
2E636TIGHT THERMAL0.070.5
2E1562MEDIUM THERMAL0.072
2E193LOOSE THERMAL0.0710
3B432TIGHT POSITIONAL0.040.05
3B1394MEDIUM POSITIONAL0.10.5
3B426LOOSE POSITIONAL0.115
3B432TIGHT THERMAL0.080.5
3B1394MEDIUM THERMAL0.092
3B426LOOSE THERMAL0.0710
4D172TIGHT POSITIONAL0.030.05
4D1638MEDIUM POSITIONAL0.050.5
4D358LOOSE POSITIONAL0.065
4D172TIGHT THERMAL0.070.5
4D1638MEDIUM THERMAL0.092
4D358LOOSE THERMAL0.0810
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 263 -
Rwork0.279 5597 -
all-5860 -
obs-21336 94.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8689-0.9162.8270.8137-0.9845.0192-0.41940.4920.8521-0.1135-0.1645-0.2377-0.56040.48130.58390.5085-0.2075-0.13980.35130.2170.385-46.70533.5993.949
23.2368-1.30341.41271.2356-0.770.9243-0.04670.2603-0.0608-0.11660.01830.06140.13270.0480.02850.4913-0.0685-0.0270.46370.06360.0564-29.2938.69723.146
34.08221.6250.51022.40430.54652.07490.1002-0.42580.2380.4299-0.2814-0.0626-0.1886-0.16670.18120.4003-0.0774-0.05880.379-0.02140.0448-79.15620.0971.747
41.66380.76651.1111.45150.32510.930.1629-0.1152-0.28290.2477-0.0381-0.20660.12790.1108-0.12470.4358-0.06450.00360.6506-0.0820.117-96.039-8.67-10.611
53.60321.6507-0.17232.4606-0.83011.8960.0336-0.3333-0.41580.3703-0.3122-0.16370.21590.12980.27850.4079-0.10240.07030.4238-0.01380.4033-40.657-25.723-1.548
61.99320.7394-1.68591.0628-0.63721.56740.1567-0.2668-0.18620.1536-0.22070.095-0.2265-0.02530.0640.4724-0.032-0.01960.62120.10510.2555-24.6013.414-13.768
72.2804-0.8876-1.13411.37190.38491.0586-0.02460.2385-0.1009-0.1119-0.0006-0.1513-0.0951-0.01810.02530.4453-0.04490.00980.3755-0.07390.1065-87.677-15.91224.955
82.5869-0.7046-2.38751.05491.13455.2322-0.33710.5976-0.6321-0.1461-0.14940.10590.494-0.60090.48640.5395-0.25130.16190.4214-0.25640.4464-72.689-39.1792.787
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 348
2X-RAY DIFFRACTION2B9 - 348
3X-RAY DIFFRACTION3C6 - 347
4X-RAY DIFFRACTION4D8 - 348
5X-RAY DIFFRACTION5E8 - 347
6X-RAY DIFFRACTION6F9 - 348
7X-RAY DIFFRACTION7G8 - 348
8X-RAY DIFFRACTION8H8 - 347

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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