[English] 日本語
Yorodumi
- PDB-5vg6: Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vg6
TitleCrystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2 in complex with NADPH and MES.
ComponentsD-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLipowska, J. / Shabalin, I.G. / Kutner, J. / Gasiorowska, O.A. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: to be published
Title: Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2 in complex with NADPH and MES.
Authors: Lipowska, J. / Shabalin, I.G. / Almo, S.C. / Minor, W.
History
DepositionApr 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
B: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
C: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
D: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
E: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
F: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
G: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
H: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
I: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
J: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)381,02629
Polymers371,81410
Non-polymers9,21119
Water48,2802680
1
A: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
J: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4397
Polymers74,3632
Non-polymers2,0775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-23 kcal/mol
Surface area24430 Å2
MethodPISA
2
B: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
C: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2446
Polymers74,3632
Non-polymers1,8814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-22 kcal/mol
Surface area24500 Å2
MethodPISA
3
D: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
H: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0495
Polymers74,3632
Non-polymers1,6863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-33 kcal/mol
Surface area22100 Å2
MethodPISA
4
E: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
I: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2446
Polymers74,3632
Non-polymers1,8814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-22 kcal/mol
Surface area24430 Å2
MethodPISA
5
F: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
G: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0495
Polymers74,3632
Non-polymers1,6863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-32 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.514, 311.036, 98.977
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
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
110B
210C
111B
211D
112B
212E
113B
213F
114B
214G
115B
215H
116B
216I
117B
217J
118C
218D
119C
219E
120C
220F
121C
221G
122C
222H
123C
223I
124C
224J
125D
225E
126D
226F
127D
227G
128D
228H
129D
229I
130D
230J
131E
231F
132E
232G
133E
233H
134E
234I
135E
235J
136F
236G
137F
237H
138F
238I
139F
239J
140G
240H
141G
241I
142G
242J
143H
243I
144H
244J
145I
245J

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
11SERSERGLYGLYAA6 - 31828 - 340
21SERSERGLYGLYBB6 - 31828 - 340
12SERSERGLYGLYAA6 - 31828 - 340
22SERSERGLYGLYCC6 - 31828 - 340
13ALAALATYRTYRAA8 - 31930 - 341
23ALAALATYRTYRDD8 - 31930 - 341
14SERSERTYRTYRAA6 - 31928 - 341
24SERSERTYRTYREE6 - 31928 - 341
15ALAALAGLYGLYAA8 - 31830 - 340
25ALAALAGLYGLYFF8 - 31830 - 340
16ALAALAGLYGLYAA78 - 318100 - 340
26ALAALAGLYGLYGG78 - 318100 - 340
17ALAALAGLYGLYAA78 - 318100 - 340
27ALAALAGLYGLYHH78 - 318100 - 340
18SERSERGLYGLYAA6 - 31828 - 340
28SERSERGLYGLYII6 - 31828 - 340
19SERSERGLYGLYAA6 - 31828 - 340
29SERSERGLYGLYJJ6 - 31828 - 340
110ALAALATYRTYRBB5 - 31927 - 341
210ALAALATYRTYRCC5 - 31927 - 341
111ALAALATYRTYRBB8 - 31930 - 341
211ALAALATYRTYRDD8 - 31930 - 341
112SERSERGLYGLYBB6 - 31828 - 340
212SERSERGLYGLYEE6 - 31828 - 340
113ALAALAGLYGLYBB8 - 31830 - 340
213ALAALAGLYGLYFF8 - 31830 - 340
114ALAALAGLYGLYBB78 - 318100 - 340
214ALAALAGLYGLYGG78 - 318100 - 340
115ALAALAGLYGLYBB78 - 318100 - 340
215ALAALAGLYGLYHH78 - 318100 - 340
116ALAALATYRTYRBB5 - 31927 - 341
216ALAALATYRTYRII5 - 31927 - 341
117ALAALATYRTYRBB5 - 31927 - 341
217ALAALATYRTYRJJ5 - 31927 - 341
118ALAALATYRTYRCC8 - 31930 - 341
218ALAALATYRTYRDD8 - 31930 - 341
119SERSERGLYGLYCC6 - 31828 - 340
219SERSERGLYGLYEE6 - 31828 - 340
120ALAALAGLYGLYCC8 - 31830 - 340
220ALAALAGLYGLYFF8 - 31830 - 340
121ALAALAGLYGLYCC78 - 318100 - 340
221ALAALAGLYGLYGG78 - 318100 - 340
122ALAALAGLYGLYCC78 - 318100 - 340
222ALAALAGLYGLYHH78 - 318100 - 340
123ALAALATYRTYRCC5 - 31927 - 341
223ALAALATYRTYRII5 - 31927 - 341
124ALAALATYRTYRCC5 - 31927 - 341
224ALAALATYRTYRJJ5 - 31927 - 341
125ALAALATYRTYRDD8 - 31930 - 341
225ALAALATYRTYREE8 - 31930 - 341
126ALAALATYRTYRDD8 - 31930 - 341
226ALAALATYRTYRFF8 - 31930 - 341
127ALAALAGLYGLYDD78 - 318100 - 340
227ALAALAGLYGLYGG78 - 318100 - 340
128ALAALAGLYGLYDD78 - 318100 - 340
228ALAALAGLYGLYHH78 - 318100 - 340
129ALAALATYRTYRDD8 - 31930 - 341
229ALAALATYRTYRII8 - 31930 - 341
130ALAALATYRTYRDD8 - 31930 - 341
230ALAALATYRTYRJJ8 - 31930 - 341
131ALAALAGLYGLYEE8 - 31830 - 340
231ALAALAGLYGLYFF8 - 31830 - 340
132ALAALAGLYGLYEE78 - 318100 - 340
232ALAALAGLYGLYGG78 - 318100 - 340
133ALAALAGLYGLYEE78 - 318100 - 340
233ALAALAGLYGLYHH78 - 318100 - 340
134SERSERGLYGLYEE6 - 31828 - 340
234SERSERGLYGLYII6 - 31828 - 340
135SERSERGLYGLYEE6 - 31828 - 340
235SERSERGLYGLYJJ6 - 31828 - 340
136ALAALAGLYGLYFF78 - 318100 - 340
236ALAALAGLYGLYGG78 - 318100 - 340
137ALAALAGLYGLYFF78 - 318100 - 340
237ALAALAGLYGLYHH78 - 318100 - 340
138ALAALAGLYGLYFF8 - 31830 - 340
238ALAALAGLYGLYII8 - 31830 - 340
139ALAALAGLYGLYFF8 - 31830 - 340
239ALAALAGLYGLYJJ8 - 31830 - 340
140ALAALATYRTYRGG78 - 319100 - 341
240ALAALATYRTYRHH78 - 319100 - 341
141ALAALAGLYGLYGG78 - 318100 - 340
241ALAALAGLYGLYII78 - 318100 - 340
142ALAALAGLYGLYGG78 - 318100 - 340
242ALAALAGLYGLYJJ78 - 318100 - 340
143ALAALAGLYGLYHH78 - 318100 - 340
243ALAALAGLYGLYII78 - 318100 - 340
144ALAALAGLYGLYHH78 - 318100 - 340
244ALAALAGLYGLYJJ78 - 318100 - 340
145ALAALATYRTYRII5 - 31927 - 341
245ALAALATYRTYRJJ5 - 31927 - 341

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

-
Components

#1: Protein
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding


Mass: 37181.441 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2) (bacteria)
Strain: ATCC BAA-1158 / Py2 / Gene: Xaut_2571 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: A7IIH0
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2680 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP, 50mM D-lactate, and 5 mM NADPH were mixed with 0.2 ul of the MCSG-2 condition #13 ...Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP, 50mM D-lactate, and 5 mM NADPH were mixed with 0.2 ul of the MCSG-2 condition #13 (0.1M MES monohydrate pH=6.5, 12%w/v PEG 20K) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 1 mg/ml TEV solution at 289 K for 1 hour

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2015
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 207487 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 35.8 Å2 / CC1/2: 0.8 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.055 / Rrim(I) all: 0.128 / Rsym value: 0.114 / Χ2: 0.897 / Net I/av σ(I): 13.7 / Net I/σ(I): 5.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
2.2-2.244.70.7531.9102510.8010.3890.850.7530.699100
2.24-2.2850.6910.8360.3450.7740.711100
2.28-2.325.20.6580.8740.3190.7340.718100
2.32-2.375.30.6240.8660.2990.6940.736100
2.37-2.425.30.5890.890.2810.6550.76100
2.42-2.485.30.4820.9160.230.5360.743100
2.48-2.545.30.4390.9370.2090.4880.758100
2.54-2.615.40.3550.950.1690.3950.775100
2.61-2.695.40.2920.9670.1390.3250.792100
2.69-2.775.40.2550.970.1220.2840.817100
2.77-2.875.40.2160.9780.1030.240.846100
2.87-2.995.40.1670.9840.080.1860.915100
2.99-3.125.40.1420.9880.0680.1580.941100
3.12-3.295.40.1160.9920.0560.1291.016100
3.29-3.495.40.0940.9930.0450.1041.057100
3.49-3.765.40.0790.9950.0380.0881.078100
3.76-4.145.30.0740.9940.0360.0821.09100
4.14-4.745.30.0680.9950.0330.0761.155100
4.74-5.975.30.0630.9960.030.071.202100
5.97-505.10.0490.9970.0240.0551.06599.8

-
Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.22data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XA8
Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.699 / SU ML: 0.154 / SU R Cruickshank DPI: 0.2347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.189
Details: U VALUES : WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. This structure has an unusually high number of RSRZ outliers because six out of ten protein chains have long ...Details: U VALUES : WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. This structure has an unusually high number of RSRZ outliers because six out of ten protein chains have long regions that are disordered, albeit visible on the electron density maps
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 10343 5 %RANDOM
Rwork0.1996 ---
obs0.2013 196974 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 202.81 Å2 / Biso mean: 57.011 Å2 / Biso min: 5.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å2-0 Å2
2--1.05 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: final / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22504 0 588 2680 25772
Biso mean--53.02 46.97 -
Num. residues----2992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01923764
X-RAY DIFFRACTIONr_bond_other_d0.0020.0222180
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.97132545
X-RAY DIFFRACTIONr_angle_other_deg1.251351035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.01452995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54422.319979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.303153411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9515229
X-RAY DIFFRACTIONr_chiral_restr0.0740.23673
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02127328
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024933
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A192680.05
12B192680.05
21A193980.05
22C193980.05
31A184420.05
32D184420.05
41A194220.04
42E194220.04
51A184100.04
52F184100.04
61A144260.04
62G144260.04
71A142740.05
72H142740.05
81A193520.05
82I193520.05
91A194480.05
92J194480.05
101B194320.04
102C194320.04
111B183000.05
112D183000.05
121B192720.04
122E192720.04
131B182740.05
132F182740.05
141B144140.04
142G144140.04
151B142880.04
152H142880.04
161B194620.04
162I194620.04
171B194200.04
172J194200.04
181C184300.05
182D184300.05
191C193360.03
192E193360.03
201C183960.05
202F183960.05
211C143960.04
212G143960.04
221C142600.04
222H142600.04
231C195500.04
232I195500.04
241C194040.05
242J194040.05
251D183720.05
252E183720.05
261D180020.05
262F180020.05
271D134800.05
272G134800.05
281D134120.05
282H134120.05
291D183480.05
292I183480.05
301D182560.05
302J182560.05
311E183760.05
312F183760.05
321E143940.04
322G143940.04
331E142880.04
332H142880.04
341E193020.04
342I193020.04
351E192260.04
352J192260.04
361F136960.05
362G136960.05
371F135940.05
372H135940.05
381F183260.05
382I183260.05
391F183040.05
392J183040.05
401G144980.03
402H144980.03
411G143680.04
412I143680.04
421G144280.04
422J144280.04
431H142780.04
432I142780.04
441H143020.04
442J143020.04
451I196020.04
452J196020.04
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 758 -
Rwork0.27 14296 -
all-15054 -
obs--99.34 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.14490.4427-0.99315.525-0.85024.2304-0.0149-0.24770.0767-0.20490.1545-0.16330.07230.522-0.13970.03090.045-0.05270.4415-0.06770.181379.02379.20755.868
23.2744-0.04951.43332.48031.47017.26870.0266-0.5421-0.0560.18050.1592-0.19020.1940.2294-0.18570.07280.0476-0.00940.4452-0.03490.175372.91577.63863.427
34.2786-0.01032.24133.12112.51427.6498-0.0209-0.22020.06870.2170.04360.1070.177-0.0218-0.02270.06290.04420.00880.3442-0.03610.165564.62180.38859.14
41.2125-0.3096-1.46442.29260.08763.52710.00940.02730.05230.09220.0972-0.1022-0.18930.1621-0.10660.0230.00160.01720.31040.0230.106662.99574.81328.231
55.6823-6.4384-1.48317.47660.72766.1741-0.1440.2566-0.45740.2074-0.23450.49740.0478-0.30930.37850.1278-0.09560.05280.3973-0.06770.241459.34762.72613.736
65.17640.50292.15553.87050.98223.3042-0.14740.23450.1109-0.1164-0.042-0.0036-0.16940.21860.18950.03990.0005-0.01080.28140.01040.08954.49381.67130.309
73.9755-0.028-4.9473.0717-0.32498.45790.2386-0.1090.36590.2436-0.08070.0174-0.57980.0187-0.15790.07650.0101-0.04460.3265-0.03250.218249.10185.0933.393
81.65840.12820.33690.6584-0.02851.4587-0.0064-0.1443-0.0495-0.0123-0.06190.00590.1547-0.12350.06830.0195-0.03160.00280.32710.01770.082852.37267.2436.676
93.29250.6788-1.11272.94260.88952.48840.0170.06890.63410.18430.11230.026-0.060.0583-0.12940.08030.0127-0.03710.3272-0.00070.206666.62388.92552.18
104.21371.84660.75564.6868-1.0286.4082-0.7207-0.6837-0.090.8898-0.1722-0.923-0.08560.28210.89290.78310.2735-0.24270.36760.14450.5945101.29525.15471.841
117.55091.7092-4.427312.5088-7.12915.9526-0.41470.1683-0.17440.65060.84050.73720.336-0.3713-0.42580.96350.1917-0.12710.49580.09160.439289.3426.05370.85
124.221-0.64781.72548.3141-3.90635.6971-0.1259-0.4845-0.32151.28540.28630.40610.4888-0.1617-0.16040.91250.24380.06520.47290.07830.270788.89130.73875.801
130.94743.1674-5.632810.7314-19.161734.28380.1206-0.2725-0.2480.4113-1.0433-0.5948-0.61271.92430.92260.58030.06090.00230.65370.07420.568496.88944.08566.73
141.2022-0.47950.44921.1803-0.42046.3774-0.03750.0944-0.0211-0.05420.07370.03770.017-0.3806-0.03620.0581-0.00290.0120.31680.02390.172588.45656.08442.384
151.4631-0.0687-0.28622.7588-0.21481.5879-0.199-0.37350.00340.53110.23680.1477-0.0243-0.1556-0.03780.21360.11760.04410.43280.01780.122783.34657.07763.101
161.4127-0.23930.35052.4952-0.21521.7921-0.1111-0.0256-0.25120.19840.17050.31580.2804-0.2997-0.05930.1197-0.01410.05290.35820.09810.232878.16644.97852.661
174.23180.38150.146313.8031-15.602946.7041-0.354-0.50110.41421.06030.0683-0.44630.54550.42440.28580.63420.1613-0.41160.35490.0850.6083103.78738.87269.801
1814.8009-9.557.75677.4609-7.2619.5076-0.5621-1.49780.43150.94590.8906-0.27440.3207-0.8553-0.32852.0864-0.0104-0.55670.73780.07610.431194.02640.73980.254
193.06120.59720.40482.0795-1.32916.2610.0343-0.1110.34760.3315-0.0770.236-0.5123-0.23270.04270.14140.02180.01950.22340.04540.18192.15285.66335.745
204.4357-1.74791.1525.9484-1.09543.9621-0.04690.38590.3929-0.0222-0.13810.0083-0.3963-0.09650.1850.1084-0.0180.02020.27310.07880.148297.94787.49528.153
215.10450.03210.29257.2498-0.59642.51060.04630.3320.23020.0703-0.1129-0.2846-0.27540.21740.06660.0784-0.0275-0.00870.27920.07220.1305105.66682.03729.876
221.3267-5.55671.369194.4395-63.28548.093-0.1778-0.44390.12676.51730.37970.0609-4.68040.9325-0.20190.8229-0.16820.2281.37080.16130.51499.98472.80445.418
232.64092.3002-0.47865.1497-1.13232.5149-0.11050.1514-0.3425-0.05510.11550.02180.3342-0.1795-0.00490.10440.00670.00950.25040.01120.160593.84945.47145.197
243.54720.579-0.5682.0908-0.47993.1813-0.0642-0.1816-0.03420.132-0.0046-0.17420.02720.17450.06890.10070.0146-0.07030.22130.00380.1698110.69256.15948.786
256.24962.00852.22985.68290.31594.50670.1014-0.0018-0.27850.1822-0.1676-0.51170.22260.62530.06620.10610.0618-0.01760.25340.00670.2249118.05352.24240.001
260.51780.0744-0.03381.6732-0.35091.0409-0.01940.0768-0.0537-0.0632-0.0221-0.04210.08180.04090.04140.0234-0.0067-0.01350.25160.01320.1006103.51260.42534.774
2718.7253-25.8262-5.614439.868116.181118.57461.37360.73042.2538-1.9984-0.2009-3.3213-0.42381.4306-1.17270.5508-0.13750.06750.57370.13460.8488116.09174.0434.718
286.6946-2.5174-2.80878.34464.05876.62930.18731.185-1.2239-1.2616-0.70060.99630.8665-1.08630.51320.7545-0.137-0.20870.6589-0.22650.64529.66338.607-7.294
296.8206-5.4394-0.448210.8316-4.22843.5351-0.19230.8892-1.6392-0.3290.05821.93550.3272-0.65190.13410.446-0.3463-0.10940.6959-0.2931.31611.03737.162-0.806
3010.3981-3.20121.497.0021-4.27572.9062-0.13641.6688-2.07840.05470.3531.51510.0539-0.3056-0.21660.5298-0.39190.27430.7806-0.38412.14691.70628.0361.26
3112.596-3.50232.06053.9633-1.46443.3906-0.9954-0.8993-1.09390.59010.06050.74630.604-0.09780.93490.67240.13380.49990.2360.1320.77827.63212.50211.714
325.3348-1.2722-2.46663.80090.61021.2454-1.1241-0.4513-1.96451.24910.02341.53560.78630.26991.10081.44860.2870.98750.3990.09381.504723.2095.29311.958
337.11590.8103-3.50595.7158-0.0984.3575-1.24060.2361-2.11620.4059-0.13120.91331.5844-0.64051.37190.8375-0.18960.6520.3634-0.07661.6028.2354.23411.069
346.2811-1.9663-4.12292.52031.20043.1169-1.8875-0.5541-2.2670.93650.42681.21831.00330.40851.46081.03690.20990.93750.21610.31421.363315.68517.74320.059
3523.9188-0.821710.92921.8582-2.55687.6548-1.22070.6024-0.4567-1.31780.7674-0.3050.9775-0.71380.45331.2319-0.4032-0.22210.9514-0.73191.57644.19425.793-10.441
3616.6907-8.62688.05915.7656-30.99267.7733-1.4226-0.098-1.58611.02811.08810.5521-1.5222-2.4050.33450.9533-0.61220.04210.7401-0.29561.8781-2.92621.0942.33
375.1712-2.8786-0.30482.8909-0.02644.1218-0.47620.4283-0.2935-0.6247-0.39040.79560.4213-0.66880.86660.8294-0.1188-0.28490.3364-0.21740.770229.47925.641-21.907
389.78111.99442.24316.96623.67298.7932-0.15440.6409-0.7376-1.1328-0.0843-0.07450.23150.12970.23860.7059-0.1033-0.07730.2249-0.05220.451538.35326.697-25.958
393.77611.95742.23787.94463.16866.49660.05150.6257-0.5864-1.0590.0718-0.16760.61610.1743-0.12320.8385-0.10390.00430.4202-0.09140.342841.95231.862-27.318
402.2495-4.5582-7.6639.355615.723126.44510.06580.4616-0.3727-0.3198-1.0580.6321-0.4854-1.73660.99220.58530.05810.00130.5344-0.06120.464233.30944.65-18.037
412.12460.82851.57241.22522.04826.1719-0.0575-0.0616-0.0997-0.04750.1008-0.07790.19920.3231-0.04340.0902-0.00980.00560.24020.02950.147240.22753.1871.68
422.18490.8963-0.55283.0404-4.11937.09470.2219-0.0975-0.03080.0034-0.18130.0136-0.22110.7745-0.04070.1704-0.0367-0.02750.4274-0.0110.172543.28258.78515.875
433.78-0.47660.34345.04560.90724.5166-0.0647-0.18420.1056-0.4033-0.01510.0279-0.2729-0.02650.07990.1495-0.06790.01050.26090.06760.099340.94560.215-9.345
441.53130.2090.062.80720.55481.5049-0.09940.0161-0.1348-0.37040.2122-0.40360.09930.2769-0.11290.1219-0.02190.06750.3241-0.01340.189551.80349.97-8.146
452.29223.61051.57997.11661.55286.3351-0.28360.40080.4994-1.73340.32311.16230.4717-0.1594-0.03951.3030.1262-0.48470.5386-0.08280.580433.01940.864-28.208
466.33673.0228-1.615810.5085-2.32986.03540.273-0.9338-0.96391.4612-0.8647-1.15610.6750.85050.59170.63890.0756-0.20520.50.23540.5107121.19139.23955.904
473.1011.7296-1.2787.72711.63755.6731-0.344-0.7268-0.78870.174-0.0195-2.09060.08310.79190.36360.34310.2467-0.11270.57550.28370.9804129.9238.23249.356
487.6664.51741.48079.40854.99032.9431-0.1583-1.6758-1.78090.28570.4185-1.57740.34170.6023-0.26010.4960.31460.30980.82130.51391.6832129.929.4146.803
498.44722.88761.1914.41220.39952.9231-0.83920.5841-0.8238-0.91120.2351-0.72010.3185-0.00120.6040.7666-0.0820.40910.1469-0.07910.5974104.40612.92836.15
508.92372.1669-0.18561.6827-1.20411.5815-0.65580.0455-1.2789-1.0688-0.1792-0.97031.0284-0.03580.8351.0290.06820.60570.1774-0.08391.1473109.175.70836.971
516.0564.8176-2.72984.0413-2.9727.3149-0.4432-0.1288-1.4704-0.3991-0.2843-0.94910.94270.64180.72750.90540.3180.74970.33040.16231.65126.4075.74835.757
522.94041.4413-0.30465.3266-0.3942.3331-0.80720.1995-1.1608-0.95950.2-1.09760.6607-0.07570.60720.9957-0.02260.82050.2307-0.09081.1733119.66516.15327.057
532.58511.69070.33395.64460.57691.6137-0.85920.0662-0.8242-0.81250.1458-0.98640.4004-0.43570.71340.7889-0.12380.52990.282-0.19880.8596111.43124.00333.592
545.26024.30720.68843.82651.729924.2064-0.4439-0.3007-0.97740.1298-0.093-1.15691.49891.47290.5370.99550.5206-0.22710.62140.56291.5677133.32224.48353.695
5510.453910.3431-2.85729.22620.20861.3607-0.20160.3943-0.934-1.2628-0.32571.20470.2157-0.29980.52721.3275-0.2792-0.05120.4986-0.08171.131981.006-12.74846.787
5612.6621.6642-2.255837.3652-3.77480.7841-1.4329-0.0748-1.7449-2.8110.3255-2.7890.55830.03461.10741.4465-0.13930.66391.0892-0.01311.846496.904-8.54346.431
572.13012.2153-1.2086.4367-2.81761.7358-0.52570.0637-0.4589-0.51730.1371-0.5280.2747-0.16550.38860.6363-0.01240.22210.212-0.03720.4516102.18320.07240.427
583.459-1.091-1.32782.5007-2.07383.806-0.36540.1557-0.3146-0.1065-0.2835-0.63930.351-0.1160.64890.64490.02720.31480.340.19780.833999.2359.02253.783
598.19534.0128-2.41854.6834-2.79753.2427-0.3147-0.3992-0.72780.3286-0.3167-0.70290.51210.25290.63150.63590.05250.20990.22850.09680.558697.5257.61259.784
601.64681.0377-0.2915.7364-1.04042.5214-0.48520.0907-0.3371-0.58190.24520.44990.4834-0.6510.240.5985-0.1050.15850.3913-0.06360.470385.14412.65347.358
615.4437-1.1265-0.197515.5586-0.53190.1233-0.63970.2633-0.3255-1.35940.3926-0.53730.2367-0.19160.24721.2396-0.31260.37780.4757-0.2920.608491.67510.00935.684
6213.1439-15.5067-1.793220.05963.2783.6677-0.0471-1.7769-0.5085-0.47361.16890.36120.59950.4379-1.12181.51270.2355-0.03911.1064-0.1230.656996.455-18.80748.51
6365.823832.8606-1.0235121.40238.635832.6254-0.9539-3.7515-5.2343-0.7913-0.26580.13570.9992-2.46951.21971.1071-0.19180.46010.77640.29631.099883.801-7.95955.936
644.5001-1.2828-3.04417.9455-6.57279.9194-0.3598-0.5312-0.98322.0245-0.1612-0.1976-0.93030.77460.5211.78580.2402-0.32170.6270.04351.70252.794-11.3631.984
6536.172827.973-1.76721.7181-2.510420.38861.52740.03760.11281.1890.0050.1850.9143-0.876-1.53240.94670.12950.28590.61420.02540.607742.304-12.356-0.774
664.3978-5.43041.438114.97882.49892.72290.06130.1098-0.52170.2291-0.16410.78350.31470.05870.10280.78840.04930.59580.24710.09911.006430.8794.7713.704
674.1083-4.728-4.81736.34524.60677.1093-0.5097-0.1401-0.53760.4160.07160.57280.25180.19170.43810.70580.05480.20270.21220.07170.542928.4825.7398.108
682.7762-1.4425-0.15175.44851.7452.3337-0.50730.1657-0.7677-0.1738-0.22340.57550.48740.20360.73060.61430.04950.34030.24070.04080.645740.13910.269-7.39
693.6932-1.1704-0.30046.05350.24483.198-0.9977-0.8021-0.5160.83640.3334-0.27870.87211.06970.66430.77010.37440.27840.54710.31790.526246.9214.3438.298
707.1390.0975-1.691411.97250.45867.3962-0.2441-0.3717-1.27210.7414-0.47710.4237-0.36680.61740.72110.97320.17860.5110.35720.37710.820138.3622.58810.834
7129.603512.62640.212313.6199-3.55361.6496-0.73394.0627-0.35250.36280.8702-0.164-0.23410.3826-0.13631.7215-0.16430.09011.43550.28270.690435.869-20.1950.026
7212.62217.39737.806317.815-9.615220.1328-0.65270.6032-2.1504-0.59770.569-2.9520.1897-0.09080.08371.33960.09330.28420.53850.12371.314146.799-9.566-7.033
732.1558-0.54050.42721.90530.16276.66520.11630.01910.2725-0.19830.0478-0.1298-0.59210.2137-0.1640.1205-0.0320.03360.2317-0.00150.181337.51685.45114.482
742.47050.20690.20655.39550.24263.49740.0751-0.1970.0752-0.1194-0.07350.1174-0.2776-0.1573-0.00170.05260.03910.01910.30630.00790.129527.14982.5818.814
752.3323-1.2194-0.578110.47911.80794.2113-0.1238-0.07060.0077-0.14380.1822-0.0349-0.06690.067-0.05830.0521-0.03080.00270.25910.02060.119632.72554.6242.936
768.4451-0.43162.72093.12270.5285.44190.0164-0.4419-0.56970.02410.13230.10590.3818-0.0337-0.14880.27490.04720.00570.22480.07920.281739.66837.5283.404
773.238-0.19550.71623.26861.25334.5853-0.03620.1832-0.1128-0.2756-0.02980.1455-0.0246-0.0810.06590.0703-0.0147-0.06340.20910.04150.144422.2554.832-0.458
786.2269-0.35730.70092.32381.16775.45830.01080.20180.0567-0.35-0.07790.2578-0.6706-1.00330.06720.22630.1348-0.04030.50750.0670.314311.12758.7524.391
790.88070.02330.29881.43380.53262.2162-0.0394-0.2041-0.11870.09520.01390.09890.1692-0.0260.02540.0581-0.0149-0.00810.25350.07290.122925.80952.32616.294
806.9308-0.64991.0953.1587-1.68081.922-0.01030.24050.2269-0.2891-0.0315-0.0042-0.214-0.22870.04190.20030.0324-0.02930.28470.00660.111125.65683.3755.431
8142.925514.5892-24.830268.965212.195237.45672.271-0.35163.67311.1002-1.32912.3003-1.9932-1.65-0.94180.54510.20170.17720.5139-0.07450.746813.4172.69814.866
822.381-0.3049-1.46555.01070.97784.08070.03840.12920.0650.09190.08330.25610.0041-0.3839-0.12160.0463-0.0441-0.07340.38220.09040.164850.84880.486-6.291
833.7126-0.10641.40922.5769-1.13724.78010.01950.2570.0481-0.3038-0.0314-0.00410.18580.13440.01190.0634-0.02850.00970.370.08250.13261.82280.253-11.315
842.5089-0.70990.36035.0526-2.4055.1708-0.0384-0.02960.0921-0.1480.14190.072-0.2005-0.2595-0.10340.0282-0.00220.01970.29590.01760.112966.7775.53620.605
854.98135.12440.82926.80431.16482.15930.0042-0.0071-0.3152-0.0967-0.0726-0.6540.12140.31020.06840.11390.02510.04380.34630.11820.228169.62560.83735.568
8613.808516.0869-5.661322.1794-10.58346.98571.0072-0.8983-0.34111.9309-1.029-0.3522-1.18930.3070.02190.71540.0746-0.13420.58150.0470.182577.90177.29532.507
871.5387-0.308-0.39552.001-0.12074.43780.08240.00460.1147-0.0776-0.07810.0432-0.2551-0.0697-0.00430.046-0.0379-0.0350.26910.05740.110276.40883.64217.467
884.58290.7868-1.75883.06440.56587.62940.2609-0.02380.7013-0.57820.0707-0.6045-0.63060.2318-0.33160.2446-0.05420.11120.37560.06980.371885.0284.1315.157
891.1133-0.28170.27920.9037-0.39221.1798-0.02330.11920.05470.017-0.0379-0.02870.01640.08210.06120.0019-0.0146-0.00190.32380.02890.090972.84172.6859.015
9010.4556-8.15763.6116.6573-0.785717.18940.79720.45561.1316-0.8422-0.4004-1.0966-1.07560.3893-0.39680.4996-0.0260.2060.66010.24260.618777.22683.696-3.451
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 41
2X-RAY DIFFRACTION2A42 - 63
3X-RAY DIFFRACTION3A64 - 98
4X-RAY DIFFRACTION4A99 - 124
5X-RAY DIFFRACTION5A125 - 140
6X-RAY DIFFRACTION6A141 - 161
7X-RAY DIFFRACTION7A162 - 189
8X-RAY DIFFRACTION8A190 - 287
9X-RAY DIFFRACTION9A288 - 319
10X-RAY DIFFRACTION10B5 - 53
11X-RAY DIFFRACTION11B54 - 65
12X-RAY DIFFRACTION12B66 - 95
13X-RAY DIFFRACTION13B96 - 103
14X-RAY DIFFRACTION14B104 - 143
15X-RAY DIFFRACTION15B144 - 209
16X-RAY DIFFRACTION16B210 - 289
17X-RAY DIFFRACTION17B290 - 297
18X-RAY DIFFRACTION18B298 - 319
19X-RAY DIFFRACTION19C5 - 41
20X-RAY DIFFRACTION20C42 - 63
21X-RAY DIFFRACTION21C64 - 96
22X-RAY DIFFRACTION22C97 - 102
23X-RAY DIFFRACTION23C103 - 138
24X-RAY DIFFRACTION24C139 - 185
25X-RAY DIFFRACTION25C186 - 199
26X-RAY DIFFRACTION26C200 - 312
27X-RAY DIFFRACTION27C313 - 319
28X-RAY DIFFRACTION28D8 - 44
29X-RAY DIFFRACTION29D45 - 84
30X-RAY DIFFRACTION30D85 - 102
31X-RAY DIFFRACTION31D103 - 129
32X-RAY DIFFRACTION32D130 - 162
33X-RAY DIFFRACTION33D163 - 192
34X-RAY DIFFRACTION34D193 - 285
35X-RAY DIFFRACTION35D286 - 307
36X-RAY DIFFRACTION36D308 - 319
37X-RAY DIFFRACTION37E6 - 48
38X-RAY DIFFRACTION38E49 - 65
39X-RAY DIFFRACTION39E66 - 95
40X-RAY DIFFRACTION40E96 - 103
41X-RAY DIFFRACTION41E104 - 127
42X-RAY DIFFRACTION42E128 - 139
43X-RAY DIFFRACTION43E140 - 169
44X-RAY DIFFRACTION44E170 - 287
45X-RAY DIFFRACTION45E288 - 319
46X-RAY DIFFRACTION46F8 - 44
47X-RAY DIFFRACTION47F45 - 84
48X-RAY DIFFRACTION48F85 - 102
49X-RAY DIFFRACTION49F103 - 129
50X-RAY DIFFRACTION50F130 - 166
51X-RAY DIFFRACTION51F167 - 194
52X-RAY DIFFRACTION52F195 - 249
53X-RAY DIFFRACTION53F250 - 294
54X-RAY DIFFRACTION54F295 - 319
55X-RAY DIFFRACTION55G78 - 94
56X-RAY DIFFRACTION56G95 - 102
57X-RAY DIFFRACTION57G103 - 140
58X-RAY DIFFRACTION58G141 - 162
59X-RAY DIFFRACTION59G163 - 186
60X-RAY DIFFRACTION60G187 - 271
61X-RAY DIFFRACTION61G272 - 287
62X-RAY DIFFRACTION62G288 - 313
63X-RAY DIFFRACTION63G314 - 319
64X-RAY DIFFRACTION64H78 - 92
65X-RAY DIFFRACTION65H93 - 98
66X-RAY DIFFRACTION66H99 - 116
67X-RAY DIFFRACTION67H117 - 143
68X-RAY DIFFRACTION68H144 - 231
69X-RAY DIFFRACTION69H232 - 278
70X-RAY DIFFRACTION70H279 - 287
71X-RAY DIFFRACTION71H288 - 309
72X-RAY DIFFRACTION72H310 - 319
73X-RAY DIFFRACTION73I5 - 43
74X-RAY DIFFRACTION74I44 - 101
75X-RAY DIFFRACTION75I102 - 122
76X-RAY DIFFRACTION76I123 - 140
77X-RAY DIFFRACTION77I141 - 171
78X-RAY DIFFRACTION78I172 - 190
79X-RAY DIFFRACTION79I191 - 287
80X-RAY DIFFRACTION80I288 - 313
81X-RAY DIFFRACTION81I314 - 319
82X-RAY DIFFRACTION82J5 - 41
83X-RAY DIFFRACTION83J42 - 98
84X-RAY DIFFRACTION84J99 - 123
85X-RAY DIFFRACTION85J124 - 138
86X-RAY DIFFRACTION86J139 - 144
87X-RAY DIFFRACTION87J145 - 176
88X-RAY DIFFRACTION88J177 - 196
89X-RAY DIFFRACTION89J197 - 314
90X-RAY DIFFRACTION90J315 - 319

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more