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- PDB-6xb9: Crystal structure of Azotobacter vinelandii 3-mercaptopropionic a... -

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Basic information

Entry
Database: PDB / ID: 6xb9
TitleCrystal structure of Azotobacter vinelandii 3-mercaptopropionic acid dioxygenase in complex with 3-hydroxypropionic acid
ComponentsCysteine dioxygenase type I protein
KeywordsOXIDOREDUCTASE / non-heme iron / competitive inhibitor / facial triad
Function / homologyCysteine dioxygenase type I / Cysteine dioxygenase type I / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / iron ion binding / 3-HYDROXY-PROPANOIC ACID / : / Cysteine dioxygenase type I protein
Function and homology information
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKiser, P.D. / Khadka, N. / Shi, W. / Pierce, B.S.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structure of 3-mercaptopropionic acid dioxygenase with a substrate analog reveals bidentate substrate binding at the iron center.
Authors: York, N.J. / Lockart, M.M. / Sardar, S. / Khadka, N. / Shi, W. / Stenkamp, R.E. / Zhang, J. / Kiser, P.D. / Pierce, B.S.
History
DepositionJun 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Cysteine dioxygenase type I protein
B: Cysteine dioxygenase type I protein
C: Cysteine dioxygenase type I protein
D: Cysteine dioxygenase type I protein
E: Cysteine dioxygenase type I protein
F: Cysteine dioxygenase type I protein
G: Cysteine dioxygenase type I protein
H: Cysteine dioxygenase type I protein
I: Cysteine dioxygenase type I protein
J: Cysteine dioxygenase type I protein
K: Cysteine dioxygenase type I protein
L: Cysteine dioxygenase type I protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,24353
Polymers280,93412
Non-polymers2,30941
Water7,116395
1
A: Cysteine dioxygenase type I protein
hetero molecules

F: Cysteine dioxygenase type I protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2099
Polymers46,8222
Non-polymers3877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3680 Å2
ΔGint-58 kcal/mol
Surface area16580 Å2
MethodPISA
2
B: Cysteine dioxygenase type I protein
G: Cysteine dioxygenase type I protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1858
Polymers46,8222
Non-polymers3636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-56 kcal/mol
Surface area17070 Å2
MethodPISA
3
H: Cysteine dioxygenase type I protein
hetero molecules

C: Cysteine dioxygenase type I protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,26911
Polymers46,8222
Non-polymers4479
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3740 Å2
ΔGint-66 kcal/mol
Surface area17050 Å2
MethodPISA
4
D: Cysteine dioxygenase type I protein
E: Cysteine dioxygenase type I protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1858
Polymers46,8222
Non-polymers3636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-57 kcal/mol
Surface area17070 Å2
MethodPISA
5
I: Cysteine dioxygenase type I protein
K: Cysteine dioxygenase type I protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1858
Polymers46,8222
Non-polymers3636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-55 kcal/mol
Surface area16720 Å2
MethodPISA
6
J: Cysteine dioxygenase type I protein
L: Cysteine dioxygenase type I protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2099
Polymers46,8222
Non-polymers3877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-56 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.219, 178.219, 75.915
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
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
112B
212C
113B
213D
114B
214E
115B
215F
116B
216G
117B
217H
118B
218I
119B
219J
120B
220K
121B
221L
122C
222D
123C
223E
124C
224F
125C
225G
126C
226H
127C
227I
128C
228J
129C
229K
130C
230L
131D
231E
132D
232F
133D
233G
134D
234H
135D
235I
136D
236J
137D
237K
138D
238L
139E
239F
140E
240G
141E
241H
142E
242I
143E
243J
144E
244K
145E
245L
146F
246G
147F
247H
148F
248I
149F
249J
150F
250K
151F
251L
152G
252H
153G
253I
154G
254J
155G
255K
156G
256L
157H
257I
158H
258J
159H
259K
160H
260L
161I
261J
162I
262K
163I
263L
164J
264K
165J
265L
166K
266L

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULYSLYSAA6 - 1976 - 197
21LEULEULYSLYSBB6 - 1976 - 197
12PROPROGLNGLNAA5 - 1955 - 195
22PROPROGLNGLNCC5 - 1955 - 195
13LEULEULYSLYSAA6 - 1976 - 197
23LEULEULYSLYSDD6 - 1976 - 197
14LEULEULYSLYSAA6 - 1976 - 197
24LEULEULYSLYSEE6 - 1976 - 197
15LEULEUGLUGLUAA6 - 1986 - 198
25LEULEUGLUGLUFF6 - 1986 - 198
16PROPROGLUGLUAA5 - 1985 - 198
26PROPROGLUGLUGG5 - 1985 - 198
17PROPROGLUGLUAA5 - 1985 - 198
27PROPROGLUGLUHH5 - 1985 - 198
18LEULEUTRPTRPAA6 - 1936 - 193
28LEULEUTRPTRPII6 - 1936 - 193
19PROPROGLUGLUAA5 - 1985 - 198
29PROPROGLUGLUJJ5 - 1985 - 198
110LEULEULYSLYSAA6 - 1976 - 197
210LEULEULYSLYSKK6 - 1976 - 197
111LEULEUTRPTRPAA6 - 1936 - 193
211LEULEUTRPTRPLL6 - 1936 - 193
112LEULEUGLNGLNBB6 - 1956 - 195
212LEULEUGLNGLNCC6 - 1956 - 195
113LEULEUGLUGLUBB6 - 1986 - 198
213LEULEUGLUGLUDD6 - 1986 - 198
114LEULEUGLUGLUBB6 - 1986 - 198
214LEULEUGLUGLUEE6 - 1986 - 198
115LEULEUGLUGLUBB6 - 1986 - 198
215LEULEUGLUGLUFF6 - 1986 - 198
116LEULEULYSLYSBB6 - 1976 - 197
216LEULEULYSLYSGG6 - 1976 - 197
117LEULEULYSLYSBB6 - 1976 - 197
217LEULEULYSLYSHH6 - 1976 - 197
118LEULEUTRPTRPBB6 - 1936 - 193
218LEULEUTRPTRPII6 - 1936 - 193
119LEULEULYSLYSBB6 - 1976 - 197
219LEULEULYSLYSJJ6 - 1976 - 197
120LEULEUGLUGLUBB6 - 1986 - 198
220LEULEUGLUGLUKK6 - 1986 - 198
121LEULEUTRPTRPBB6 - 1936 - 193
221LEULEUTRPTRPLL6 - 1936 - 193
122LEULEUGLNGLNCC6 - 1956 - 195
222LEULEUGLNGLNDD6 - 1956 - 195
123LEULEUGLNGLNCC6 - 1956 - 195
223LEULEUGLNGLNEE6 - 1956 - 195
124LEULEUSERSERCC6 - 1966 - 196
224LEULEUSERSERFF6 - 1966 - 196
125PROPROGLNGLNCC5 - 1955 - 195
225PROPROGLNGLNGG5 - 1955 - 195
126PROPROGLNGLNCC5 - 1955 - 195
226PROPROGLNGLNHH5 - 1955 - 195
127LEULEUTRPTRPCC6 - 1936 - 193
227LEULEUTRPTRPII6 - 1936 - 193
128PROPROGLNGLNCC5 - 1955 - 195
228PROPROGLNGLNJJ5 - 1955 - 195
129LEULEUGLNGLNCC6 - 1956 - 195
229LEULEUGLNGLNKK6 - 1956 - 195
130LEULEUTRPTRPCC6 - 1936 - 193
230LEULEUTRPTRPLL6 - 1936 - 193
131LEULEUGLUGLUDD6 - 1986 - 198
231LEULEUGLUGLUEE6 - 1986 - 198
132LEULEUGLUGLUDD6 - 1986 - 198
232LEULEUGLUGLUFF6 - 1986 - 198
133LEULEULYSLYSDD6 - 1976 - 197
233LEULEULYSLYSGG6 - 1976 - 197
134LEULEULYSLYSDD6 - 1976 - 197
234LEULEULYSLYSHH6 - 1976 - 197
135LEULEUTRPTRPDD6 - 1936 - 193
235LEULEUTRPTRPII6 - 1936 - 193
136LEULEULYSLYSDD6 - 1976 - 197
236LEULEULYSLYSJJ6 - 1976 - 197
137LEULEUGLUGLUDD6 - 1986 - 198
237LEULEUGLUGLUKK6 - 1986 - 198
138LEULEUTRPTRPDD6 - 1936 - 193
238LEULEUTRPTRPLL6 - 1936 - 193
139LEULEUGLUGLUEE6 - 1986 - 198
239LEULEUGLUGLUFF6 - 1986 - 198
140LEULEULYSLYSEE6 - 1976 - 197
240LEULEULYSLYSGG6 - 1976 - 197
141LEULEULYSLYSEE6 - 1976 - 197
241LEULEULYSLYSHH6 - 1976 - 197
142LEULEUTRPTRPEE6 - 1936 - 193
242LEULEUTRPTRPII6 - 1936 - 193
143LEULEULYSLYSEE6 - 1976 - 197
243LEULEULYSLYSJJ6 - 1976 - 197
144LEULEUGLUGLUEE6 - 1986 - 198
244LEULEUGLUGLUKK6 - 1986 - 198
145LEULEUTRPTRPEE6 - 1936 - 193
245LEULEUTRPTRPLL6 - 1936 - 193
146LEULEUGLUGLUFF6 - 1986 - 198
246LEULEUGLUGLUGG6 - 1986 - 198
147LEULEUGLUGLUFF6 - 1986 - 198
247LEULEUGLUGLUHH6 - 1986 - 198
148LEULEUASPASPFF6 - 1946 - 194
248LEULEUASPASPII6 - 1946 - 194
149LEULEUGLUGLUFF6 - 1986 - 198
249LEULEUGLUGLUJJ6 - 1986 - 198
150LEULEUGLUGLUFF6 - 1986 - 198
250LEULEUGLUGLUKK6 - 1986 - 198
151LEULEUASPASPFF6 - 1946 - 194
251LEULEUASPASPLL6 - 1946 - 194
152PROPROGLUGLUGG5 - 1985 - 198
252PROPROGLUGLUHH5 - 1985 - 198
153LEULEUTRPTRPGG6 - 1936 - 193
253LEULEUTRPTRPII6 - 1936 - 193
154PROPROGLUGLUGG5 - 1985 - 198
254PROPROGLUGLUJJ5 - 1985 - 198
155LEULEULYSLYSGG6 - 1976 - 197
255LEULEULYSLYSKK6 - 1976 - 197
156LEULEUTRPTRPGG6 - 1936 - 193
256LEULEUTRPTRPLL6 - 1936 - 193
157LEULEUTRPTRPHH6 - 1936 - 193
257LEULEUTRPTRPII6 - 1936 - 193
158PROPROGLUGLUHH5 - 1985 - 198
258PROPROGLUGLUJJ5 - 1985 - 198
159LEULEULYSLYSHH6 - 1976 - 197
259LEULEULYSLYSKK6 - 1976 - 197
160LEULEUTRPTRPHH6 - 1936 - 193
260LEULEUTRPTRPLL6 - 1936 - 193
161LEULEUTRPTRPII6 - 1936 - 193
261LEULEUTRPTRPJJ6 - 1936 - 193
162LEULEUTRPTRPII6 - 1936 - 193
262LEULEUTRPTRPKK6 - 1936 - 193
163LEULEUASPASPII6 - 1946 - 194
263LEULEUASPASPLL6 - 1946 - 194
164LEULEULYSLYSJJ6 - 1976 - 197
264LEULEULYSLYSKK6 - 1976 - 197
165LEULEUTRPTRPJJ6 - 1936 - 193
265LEULEUTRPTRPLL6 - 1936 - 193
166LEULEUTRPTRPKK6 - 1936 - 193
266LEULEUTRPTRPLL6 - 1936 - 193

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

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Cysteine dioxygenase type I protein


Mass: 23411.135 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C1DN94

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Non-polymers , 5 types, 436 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-3OH / 3-HYDROXY-PROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES-NaOH, pH 6, 30 % w/v poly(acrylic acid sodium salt) 5100, 10 % v/v ethanol, 50 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979339 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979339 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.663
11K, H, -L20.337
ReflectionResolution: 2.25→50 Å / Num. obs: 127973 / % possible obs: 99.9 % / Redundancy: 4.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.35
Reflection shellResolution: 2.25→2.39 Å / Rmerge(I) obs: 1.642 / Mean I/σ(I) obs: 0.78 / Num. unique obs: 20673 / CC1/2: 0.484

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TLF
Resolution: 2.25→46.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.253 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 6243 4.9 %RANDOM
Rwork0.1956 ---
obs0.1971 121709 99.84 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 132.81 Å2 / Biso mean: 52.731 Å2 / Biso min: 31.04 Å2
Baniso -1Baniso -2Baniso -3
1-15.91 Å20 Å20 Å2
2--15.91 Å20 Å2
3----31.81 Å2
Refinement stepCycle: final / Resolution: 2.25→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18363 0 101 395 18859
Biso mean--54.19 50.14 -
Num. residues----2303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01319012
X-RAY DIFFRACTIONr_bond_other_d0.0010.01717099
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.64225734
X-RAY DIFFRACTIONr_angle_other_deg1.1351.5839538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12352290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.92620.6461223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.913152921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.77715214
X-RAY DIFFRACTIONr_chiral_restr0.0480.22234
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221706
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024392
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A62240.05
12B62240.05
21A62140.03
22C62140.03
31A62440.05
32D62440.05
41A62580.04
42E62580.04
51A61110.04
52F61110.04
61A63280.04
62G63280.04
71A63100.03
72H63100.03
81A61360.04
82I61360.04
91A62940.05
92J62940.05
101A62250.05
102K62250.05
111A60830.04
112L60830.04
121B62290.03
122C62290.03
131B62380.06
132D62380.06
141B63240.03
142E63240.03
151B61140.04
152F61140.04
161B62410.04
162G62410.04
171B62130.04
172H62130.04
181B61520.03
182I61520.03
191B62460.03
192J62460.03
201B62390.05
202K62390.05
211B60900.04
212L60900.04
221C61690.04
222D61690.04
231C62510.02
232E62510.02
241C60500.03
242F60500.03
251C62200.03
252G62200.03
261C62100.03
262H62100.03
271C61670.03
272I61670.03
281C62060.03
282J62060.03
291C61780.04
292K61780.04
301C61060.03
302L61060.03
311D63030.04
312E63030.04
321D61230.03
322F61230.03
331D63010.04
332G63010.04
341D62920.03
342H62920.03
351D61530.05
352I61530.05
361D62790.05
362J62790.05
371D62910.05
372K62910.05
381D61110.04
382L61110.04
391E61380.03
392F61380.03
401E62660.04
402G62660.04
411E62440.03
412H62440.03
421E61830.04
422I61830.04
431E62500.03
432J62500.03
441E62730.04
442K62730.04
451E61110.04
452L61110.04
461F61220.03
462G61220.03
471F61060.03
472H61060.03
481F59980.03
482I59980.03
491F60990.04
492J60990.04
501F60820.04
502K60820.04
511F59680.04
512L59680.04
521G63540.02
522H63540.02
531G61490.04
532I61490.04
541G63410.04
542J63410.04
551G62600.04
552K62600.04
561G61090.04
562L61090.04
571H61520.04
572I61520.04
581H63220.04
582J63220.04
591H62410.04
592K62410.04
601H60960.04
602L60960.04
611I61410.04
612J61410.04
621I61180.05
622K61180.05
631I61310.05
632L61310.05
641J62380.04
642K62380.04
651J61010.04
652L61010.04
661K60600.05
662L60600.05
LS refinement shellResolution: 2.25→2.307 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.331 460 -
Rwork0.281 8982 -
obs--99.18 %

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