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- PDB-2grj: Crystal structure of Dephospho-CoA kinase (EC 2.7.1.24) (Dephosph... -

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Basic information

Entry
Database: PDB / ID: 2grj
TitleCrystal structure of Dephospho-CoA kinase (EC 2.7.1.24) (Dephosphocoenzyme A kinase) (tm1387) from THERMOTOGA MARITIMA at 2.60 A resolution
ComponentsDephospho-CoA kinase
KeywordsTRANSFERASE / tm1387 / Dephospho-CoA kinase / EC 2.7.1.24 / Dephosphocoenzyme A kinase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Dephospho-CoA kinase / Dephospho-CoA kinase / Dephospho-CoA kinase (DPCK) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DEPHOSPHO COENZYME A / Dephospho-CoA kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Dephospho-CoA kinase (EC 2.7.1.24) (Dephosphocoenzyme A kinase) (tm1387) from THERMOTOGA MARITIMA at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH ...BIOMOLECULE: 1, 2, 3, 4, 5, 6, 7, 8 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dephospho-CoA kinase
B: Dephospho-CoA kinase
C: Dephospho-CoA kinase
D: Dephospho-CoA kinase
E: Dephospho-CoA kinase
F: Dephospho-CoA kinase
G: Dephospho-CoA kinase
H: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,56528
Polymers176,5058
Non-polymers9,06020
Water1,20767
1
A: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1783
Polymers22,0631
Non-polymers1,1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1783
Polymers22,0631
Non-polymers1,1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2134
Polymers22,0631
Non-polymers1,1503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1783
Polymers22,0631
Non-polymers1,1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2495
Polymers22,0631
Non-polymers1,1864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1783
Polymers22,0631
Non-polymers1,1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1783
Polymers22,0631
Non-polymers1,1152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2134
Polymers22,0631
Non-polymers1,1503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.832, 87.217, 98.586
Angle α, β, γ (deg.)90.000, 106.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91A
101B
111C
121D
131E
141F
151G
161H
171A
181B
191C
201D
211E
221F
231G
241H
12A
22B
32C
42D
52E
62F
72H

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISSERAA-1 - 5311 - 65
211HISSERBB-1 - 5311 - 65
311HISSERCC-1 - 5311 - 65
411HISSERDD-1 - 5311 - 65
511HISSEREE-1 - 5311 - 65
611HISSERFF-1 - 5311 - 65
711HISSERGG-1 - 5311 - 65
811HISSERHH-1 - 5311 - 65
921ASNARGAA61 - 13473 - 146
1021ASNARGBB61 - 13473 - 146
1121ASNARGCC61 - 13473 - 146
1221ASNARGDD61 - 13473 - 146
1321ASNARGEE61 - 13473 - 146
1421ASNARGFF61 - 13473 - 146
1521ASNARGGG61 - 13473 - 146
1621ASNARGHH61 - 13473 - 146
1731ASPVALAA139 - 175151 - 187
1831ASPVALBB139 - 175151 - 187
1931ASPVALCC139 - 175151 - 187
2031ASPVALDD139 - 175151 - 187
2131ASPVALEE139 - 175151 - 187
2231ASPVALFF139 - 175151 - 187
2331ASPVALGG139 - 175151 - 187
2431ASPVALHH139 - 175151 - 187
112ASNALAAA135 - 138147 - 150
212ASNALABB135 - 138147 - 150
312ASNALACC135 - 138147 - 150
412ASNALADD135 - 138147 - 150
512ASNALAEE135 - 138147 - 150
612ASNALAFF135 - 138147 - 150
712ASNALAHH135 - 138147 - 150

NCS ensembles :
ID
1
2
DetailsSIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Dephospho-CoA kinase / Dephosphocoenzyme A kinase


Mass: 22063.102 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: coaE / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1A7, dephospho-CoA kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-COD / DEPHOSPHO COENZYME A


Mass: 687.554 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H35N7O13P2S
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.1 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.2
Details: 30.0M NaCl, 32.5% PEG-8000, 0.1M Na,K-Phosphate pH 5.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.97921, 0.9537246, 0.97907
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 13, 2003
RadiationMonochromator: Bent cylindrical Si-mirror (Rh coating) Diamond(111) double-bounce monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.95372461
30.979071
ReflectionResolution: 2.6→47.7 Å / Num. obs: 44701 / % possible obs: 96.8 % / Redundancy: 3.37 % / Biso Wilson estimate: 40.15 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.79
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID
2.6-2.6974.70.3751.841
2.69-2.897.10.2822.471
2.8-2.9399.80.2273.181
2.93-3.0899.90.1714.131
3.08-3.2799.90.125.481
3.27-3.5299.80.0887.241
3.52-3.8899.90.069.891
3.88-4.4399.70.04911.81
4.43-5.5799.30.04512.41
5.57-47.797.70.0412.21

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→25.29 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / SU B: 20.266 / SU ML: 0.233 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.34
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THERE IS A DEPHOSPHO-COA MOLECULE AND AN ADP MOLECULE BOUND IN EACH MONOMER. 3. FOUR CHLORIDE IONS FROM CRYSTALLIZATION SOLUTION HAVE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THERE IS A DEPHOSPHO-COA MOLECULE AND AN ADP MOLECULE BOUND IN EACH MONOMER. 3. FOUR CHLORIDE IONS FROM CRYSTALLIZATION SOLUTION HAVE BEEN INCLUDED IN THE MODEL. 4. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2249 5 %RANDOM
Rwork0.191 ---
all0.193 ---
obs0.19328 44609 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.699 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å21.01 Å2
2---1.92 Å20 Å2
3---1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10846 0 572 67 11485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02211550
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211094
X-RAY DIFFRACTIONr_angle_refined_deg1.7912.03215677
X-RAY DIFFRACTIONr_angle_other_deg0.899325593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62251424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.13224.769411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.457152107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.291563
X-RAY DIFFRACTIONr_chiral_restr0.0850.21923
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212261
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022078
X-RAY DIFFRACTIONr_nbd_refined0.2290.22231
X-RAY DIFFRACTIONr_nbd_other0.1770.210794
X-RAY DIFFRACTIONr_nbtor_refined0.1760.25533
X-RAY DIFFRACTIONr_nbtor_other0.0880.27548
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.140.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.27
X-RAY DIFFRACTIONr_mcbond_it1.74237728
X-RAY DIFFRACTIONr_mcbond_other0.25132968
X-RAY DIFFRACTIONr_mcangle_it2.158511392
X-RAY DIFFRACTIONr_scbond_it4.64584853
X-RAY DIFFRACTIONr_scangle_it6.649114285
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A982TIGHT POSITIONAL0.060.05
12B982TIGHT POSITIONAL0.040.05
13C982TIGHT POSITIONAL0.050.05
14D982TIGHT POSITIONAL0.050.05
15E982TIGHT POSITIONAL0.040.05
16F982TIGHT POSITIONAL0.050.05
17G982TIGHT POSITIONAL0.050.05
18H982TIGHT POSITIONAL0.050.05
11A1409MEDIUM POSITIONAL0.390.5
12B1409MEDIUM POSITIONAL0.390.5
13C1409MEDIUM POSITIONAL0.350.5
14D1409MEDIUM POSITIONAL0.410.5
15E1409MEDIUM POSITIONAL0.370.5
16F1409MEDIUM POSITIONAL0.480.5
17G1409MEDIUM POSITIONAL0.340.5
18H1409MEDIUM POSITIONAL0.520.5
11A982TIGHT THERMAL0.120.5
12B982TIGHT THERMAL0.110.5
13C982TIGHT THERMAL0.10.5
14D982TIGHT THERMAL0.110.5
15E982TIGHT THERMAL0.10.5
16F982TIGHT THERMAL0.110.5
17G982TIGHT THERMAL0.10.5
18H982TIGHT THERMAL0.110.5
11A1409MEDIUM THERMAL0.732
12B1409MEDIUM THERMAL0.72
13C1409MEDIUM THERMAL0.72
14D1409MEDIUM THERMAL0.732
15E1409MEDIUM THERMAL0.662
16F1409MEDIUM THERMAL0.732
17G1409MEDIUM THERMAL0.662
18H1409MEDIUM THERMAL0.712
21A24TIGHT POSITIONAL0.040.05
22B24TIGHT POSITIONAL0.030.05
23C24TIGHT POSITIONAL0.050.05
24D24TIGHT POSITIONAL0.040.05
25E24TIGHT POSITIONAL0.040.05
26F24TIGHT POSITIONAL0.050.05
27H24TIGHT POSITIONAL0.040.05
21A19MEDIUM POSITIONAL0.180.5
22B19MEDIUM POSITIONAL0.210.5
23C19MEDIUM POSITIONAL0.160.5
24D19MEDIUM POSITIONAL0.230.5
25E19MEDIUM POSITIONAL0.210.5
26F19MEDIUM POSITIONAL0.220.5
27H19MEDIUM POSITIONAL0.20.5
21A24TIGHT THERMAL0.110.5
22B24TIGHT THERMAL0.080.5
23C24TIGHT THERMAL0.150.5
24D24TIGHT THERMAL0.090.5
25E24TIGHT THERMAL0.120.5
26F24TIGHT THERMAL0.120.5
27H24TIGHT THERMAL0.10.5
21A19MEDIUM THERMAL0.722
22B19MEDIUM THERMAL0.442
23C19MEDIUM THERMAL0.522
24D19MEDIUM THERMAL0.392
25E19MEDIUM THERMAL0.662
26F19MEDIUM THERMAL0.482
27H19MEDIUM THERMAL0.622
LS refinement shellResolution: 2.6→2.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 150 -
Rwork0.313 2669 -
obs-2819 84.5 %
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)
12.67580.20170.22842.3260.75951.2854-0.09050.118-0.0012-0.02340.0823-0.0693-0.0577-0.0920.0081-0.09770.0451-0.0202-0.1810.0138-0.115751.2753-15.9922-45.5972
24.1390.7156-1.34684.870.17423.30360.1418-0.52860.44250.6204-0.20160.53170.2092-0.52930.05980.08720.04270.06620.1076-0.0393-0.039237.254-10.7948-27.9646
33.5830.26460.34732.62240.68542.4665-0.0303-0.01330.10320.11650.08490.0908-0.1059-0.0282-0.0546-0.12730.00640.0043-0.21850.0311-0.076751.08176.8087-47.2838
47.01061.03160.35274.37671.32973.8751-0.03680.8793-0.2077-0.5182-0.01820.8027-0.0147-0.44640.055-0.0323-0.0004-0.11630.0940.02210.047233.48132.274-61.226
52.54050.28920.33153.13590.99212.5692-0.07370.0845-0.04730.05950.0290.24560.2247-0.11910.0448-0.07390.00980.0044-0.1693-0.0028-0.10725.877-14.608-45.4016
63.5585-0.7048-1.41272.4420.49711.0485-0.2261-0.54370.09391.0859-0.02231.01430.1415-0.66480.24840.2946-0.0040.23120.2281-0.04410.1988-7.7085-9.2024-27.5692
72.3966-0.12830.42962.3025-0.0261.7301-0.0348-0.06860.02620.19620.04320.0271-0.1154-0.0533-0.0084-0.10740.00310.0092-0.13110.0192-0.1416.01198.2192-47.4874
86.3948-0.7378-2.49295.68970.13055.34280.01690.5881-0.3621-0.6657-0.04340.89980.3082-0.70060.0265-0.0705-0.0128-0.08460.1294-0.01540.0548-11.39883.8142-61.6332
94.13330.2382-0.67194.4654-1.31592.5392-0.12680.15260.041-0.2180.026-0.2830.04360.06020.1008-0.07650.01580.0487-0.1658-0.0259-0.11137.989319.2584-0.2544
103.9653-0.82250.62773.6259-1.6026.9953-0.1187-0.3649-0.08330.8665-0.1824-1.56380.00451.04890.30110.0757-0.0152-0.22390.17740.13580.364925.558414.988414.4356
113.5987-0.2542-0.02713.0445-0.45932.5617-0.0184-0.16880.00760.06320.05180.0652-0.03480.1175-0.0334-0.1263-0.0075-0.009-0.1588-0.0378-0.13979.0369-3.8364-1.1327
125.8875-1.2429-1.09472.14491.19944.9610.27190.31830.4609-0.71790.0105-0.6308-0.26480.3142-0.28250.0417-0.00140.10580.0585-0.0354-0.006824.22711.2911-17.4738
133.35250.6096-0.13083.4021-0.77621.843-0.1026-0.0343-0.253-0.05830.1389-0.3450.0350.1326-0.0363-0.0365-0.0287-0.0288-0.0917-0.0662-0.030454.3917-2.3856-1.6111
147.12891.703-2.89535.941-1.27945.338-0.25280.4944-0.0386-1.47270.0353-1.16640.0898-0.04840.21750.3082-0.07270.2260.1797-0.12540.158969.1483.8239-18.2792
153.56140.574-0.92732.2143-0.2932.3417-0.06720.0749-0.0254-0.20450.10750.13090.02910.0815-0.0403-0.10370.0003-0.0064-0.1235-0.0346-0.104153.1220.329-0.1744
166.13850.83281.6125.1709-0.92984.4958-0.1928-0.8727-0.3380.76690.3581-0.44230.59671.0189-0.16530.03860.17280.01360.4520.0489-0.012970.623515.865613.6585
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-2 - 3710 - 49
21AA84 - 17696 - 188
32AA38 - 8350 - 95
43BB-2 - 3710 - 49
53BB84 - 17696 - 188
64BB38 - 8350 - 95
75CC-2 - 3710 - 49
85CC84 - 17696 - 188
96CC38 - 8350 - 95
107DD-2 - 3710 - 49
117DD84 - 17696 - 188
128DD38 - 8350 - 95
139EE-2 - 3710 - 49
149EE84 - 17696 - 188
1510EE38 - 8350 - 95
1611FF-2 - 3710 - 49
1711FF84 - 17696 - 188
1812FF38 - 8350 - 95
1913GG-2 - 3710 - 49
2013GG84 - 17696 - 188
2114GG38 - 8350 - 95
2215HH-2 - 3710 - 49
2315HH84 - 17696 - 188
2416HH38 - 8350 - 95

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