[English] 日本語
Yorodumi
- PDB-4pn3: Crystal structure of 3-hydroxyacyl-CoA-dehydrogenase from Brucell... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pn3
TitleCrystal structure of 3-hydroxyacyl-CoA-dehydrogenase from Brucella melitensis
Components3-hydroxyacyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesBrucella melitensis 64/150 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLukacs, C.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of 3-hydroxyacyl-CoA-dehydrogenase from Brucella melitensis
Authors: Lukacs, C.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D.
History
DepositionMay 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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: 3-hydroxyacyl-CoA dehydrogenase
B: 3-hydroxyacyl-CoA dehydrogenase
C: 3-hydroxyacyl-CoA dehydrogenase
D: 3-hydroxyacyl-CoA dehydrogenase
E: 3-hydroxyacyl-CoA dehydrogenase
F: 3-hydroxyacyl-CoA dehydrogenase
G: 3-hydroxyacyl-CoA dehydrogenase
H: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,06812
Polymers218,5808
Non-polymers4894
Water8,953497
1
A: 3-hydroxyacyl-CoA dehydrogenase
B: 3-hydroxyacyl-CoA dehydrogenase
C: 3-hydroxyacyl-CoA dehydrogenase
D: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5346
Polymers109,2904
Non-polymers2442
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-101 kcal/mol
Surface area33560 Å2
MethodPISA
2
E: 3-hydroxyacyl-CoA dehydrogenase
F: 3-hydroxyacyl-CoA dehydrogenase
G: 3-hydroxyacyl-CoA dehydrogenase
H: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5346
Polymers109,2904
Non-polymers2442
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-102 kcal/mol
Surface area33390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.840, 72.840, 350.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA-4 - 2554 - 263
21LYSLYSBB-4 - 2554 - 263
12ALAALAAA-3 - 2545 - 262
22ALAALACC-3 - 2545 - 262
13LYSLYSAA-4 - 2554 - 263
23LYSLYSDD-4 - 2554 - 263
14ALAALAAA-1 - 2547 - 262
24ALAALAEE-1 - 2547 - 262
15LYSLYSAA-3 - 2555 - 263
25LYSLYSFF-3 - 2555 - 263
16ALAALAAA0 - 2548 - 262
26ALAALAGG0 - 2548 - 262
17LYSLYSAA-4 - 2554 - 263
27LYSLYSHH-4 - 2554 - 263
18ALAALABB-3 - 2545 - 262
28ALAALACC-3 - 2545 - 262
19LYSLYSBB-4 - 2554 - 263
29LYSLYSDD-4 - 2554 - 263
110ALAALABB-1 - 2547 - 262
210ALAALAEE-1 - 2547 - 262
111LYSLYSBB-3 - 2555 - 263
211LYSLYSFF-3 - 2555 - 263
112ALAALABB0 - 2548 - 262
212ALAALAGG0 - 2548 - 262
113LYSLYSBB-4 - 2554 - 263
213LYSLYSHH-4 - 2554 - 263
114LYSLYSCC-3 - 2555 - 263
214LYSLYSDD-3 - 2555 - 263
115ALAALACC-1 - 2547 - 262
215ALAALAEE-1 - 2547 - 262
116LYSLYSCC-3 - 2555 - 263
216LYSLYSFF-3 - 2555 - 263
117ALAALACC0 - 2548 - 262
217ALAALAGG0 - 2548 - 262
118LYSLYSCC-3 - 2555 - 263
218LYSLYSHH-3 - 2555 - 263
119LYSLYSDD-1 - 2557 - 263
219LYSLYSEE-1 - 2557 - 263
120LYSLYSDD-3 - 2555 - 263
220LYSLYSFF-3 - 2555 - 263
121LYSLYSDD0 - 2558 - 263
221LYSLYSGG0 - 2558 - 263
122ALAALADD-4 - 2544 - 262
222ALAALAHH-4 - 2544 - 262
123LYSLYSEE-1 - 2557 - 263
223LYSLYSFF-1 - 2557 - 263
124ALAALAEE0 - 2548 - 262
224ALAALAGG0 - 2548 - 262
125LYSLYSEE-1 - 2557 - 263
225LYSLYSHH-1 - 2557 - 263
126LYSLYSFF0 - 2558 - 263
226LYSLYSGG0 - 2558 - 263
127LYSLYSFF-3 - 2555 - 263
227LYSLYSHH-3 - 2555 - 263
128LYSLYSGG0 - 2558 - 263
228LYSLYSHH0 - 2558 - 263

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

-
Components

#1: Protein
3-hydroxyacyl-CoA dehydrogenase /


Mass: 27322.477 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis 64/150 (bacteria) / Gene: C045_02890 / Production host: Escherichia coli (E. coli) / References: UniProt: N7K0F6
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: JCSG+ f4: 0.1M Hepes pH6.5, 20% Jeffamine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.547
11K, H, -L20.453
ReflectionResolution: 2.15→50 Å / Num. obs: 96319 / % possible obs: 97.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 11
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 5 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3.6 / % possible all: 99.6

-
Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TPC
Resolution: 2.15→47.13 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.853 / SU B: 14.444 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26393 1885 2 %RANDOM
Rwork0.23631 ---
obs0.23685 94319 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.974 Å2
Baniso -1Baniso -2Baniso -3
1--5.27 Å20 Å2-0 Å2
2---5.27 Å2-0 Å2
3---10.55 Å2
Refinement stepCycle: 1 / Resolution: 2.15→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14442 0 32 497 14971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01914685
X-RAY DIFFRACTIONr_bond_other_d0.0090.0214367
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9619911
X-RAY DIFFRACTIONr_angle_other_deg1.352332748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65652036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80323.653542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.671152229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.61815106
X-RAY DIFFRACTIONr_chiral_restr0.0760.22346
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02117240
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023222
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_it1.0581.2658175
X-RAY DIFFRACTIONr_mcbond_other1.0581.2658173
X-RAY DIFFRACTIONr_mcangle_it1.7361.89310198
X-RAY DIFFRACTIONr_mcangle_other1.7361.89310199
X-RAY DIFFRACTIONr_scbond_it1.0141.2936510
X-RAY DIFFRACTIONr_scbond_other1.0141.2936510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.621.9199714
X-RAY DIFFRACTIONr_long_range_B_refined3.7910.00816181
X-RAY DIFFRACTIONr_long_range_B_other3.7039.9516079
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)
11A141800.08
12B141800.08
21A139980.08
22C139980.08
31A136640.08
32D136640.08
41A142530.08
42E142530.08
51A138860.08
52F138860.08
61A138300.08
62G138300.08
71A135860.07
72H135860.07
81B138090.07
82C138090.07
91B133020.08
92D133020.08
101B143240.06
102E143240.06
111B138840.07
112F138840.07
121B138460.07
122G138460.07
131B134220.07
132H134220.07
141C132130.07
142D132130.07
151C140960.06
152E140960.06
161C139660.07
162F139660.07
171C137540.07
172G137540.07
181C133990.07
182H133990.07
191D135080.07
192E135080.07
201D133880.07
202F133880.07
211D133170.08
212G133170.08
221D133230.07
222H133230.07
231E139420.06
232F139420.06
241E141140.07
242G141140.07
251E135000.06
252H135000.06
261F137030.07
262G137030.07
271F136200.06
272H136200.06
281G134310.06
282H134310.06
LS refinement shellResolution: 2.15→2.206 Å
RfactorNum. reflection% reflection
Rfree0.296 145 5 %
Rwork0.274 7091 -
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)
10.46420.15280.08390.3653-0.06570.0472-0.0524-0.04420.0790.10240.0093-0.1654-0.0741-0.01190.04310.2874-0.06090.05710.1405-0.02070.229498.459251.1935-20.4107
20.29470.4345-0.28890.6559-0.51011.0496-0.04240.0031-0.0502-0.01880.0164-0.0795-0.0451-0.01840.0260.2475-0.00320.04640.16530.00130.202189.809444.3314-25.3807
30.3613-0.27740.17750.6717-0.3770.8232-0.0346-0.0052-0.02740.09040.0782-0.064-0.03820.076-0.04370.2166-0.03250.03920.14750.01360.2474100.252533.9723-16.2318
40.2139-0.0922-0.26770.6005-0.00440.4715-0.0586-0.0453-0.0632-0.251-0.0144-0.1810.09170.02550.0730.2612-0.00870.09170.1008-0.02160.292104.09214.6945-36.0455
54.66620.20611.67510.43130.29460.9287-0.0250.1316-0.1709-0.13340.01440.01380.0360.11160.01060.2306-0.00980.01640.15010.01070.269692.74899.6463-29.6827
60.33960.05010.03970.4674-0.04320.4654-0.03960.0034-0.0622-0.15660.0251-0.04190.0197-0.00640.01450.2507-0.03180.05760.1191-0.01830.256392.34424.9198-32.4325
72.7061-0.42980.83490.0896-0.37173.12240.2025-0.3679-0.3423-0.04820.04020.03910.1573-0.4496-0.24270.1547-0.1235-0.03720.15140.12840.43459.32669.8239-15.7256
83.1065-0.3178-0.65680.06590.01860.2197-0.0221-0.0781-0.4946-0.08330.01360.1320.13680.01810.00850.3068-0.0477-0.08940.04570.03310.449972.48292.1817-20.847
90.3711-0.38850.1830.5029-0.01990.45140.0383-0.1012-0.1839-0.0750.0730.1269-0.0622-0.1077-0.11130.1786-0.0471-0.00830.18880.07180.295372.459516.5817-17.6428
100.1977-1.20210.06668.3145-0.58040.06560.0685-0.00890.04240.1096-0.00990.0582-0.0551-0.0477-0.05860.2475-0.00660.08480.33260.0460.275459.79823.342-0.233
110.38620.1638-0.1860.2379-0.19890.2147-0.0159-0.0760.0277-0.0020.09860.0707-0.0935-0.0695-0.08270.24530.05360.06620.2120.06310.182567.695943.5585-9.3689
120.241-0.19310.26790.40380.12491.03150.0838-0.0674-0.1104-0.0290.12750.0729-0.0826-0.0784-0.21130.21540.01470.03590.22730.07330.18867.057131.8281-17.3199
131.53480.0344-0.68141.3828-0.53830.53790.0333-0.11530.38990.01630.10050.00310.02930.0825-0.13380.1642-0.02150.03140.2107-0.04890.296783.149168.348-59.1069
141.22050.61380.45961.00510.840.76260.06020.07240.1341-0.10610.0639-0.0765-0.05820.1637-0.12410.2158-0.00470.01140.2555-0.0250.147590.859559.8399-69.4505
150.5895-0.3170.49140.4019-0.01330.76660.00420.0540.0927-0.0047-0.0118-0.0056-0.00320.06270.00760.1639-0.0190.01280.2273-0.03320.237177.101957.2715-65.617
160.7625-0.1774-0.11370.15220.02380.22420.0136-0.18970.1302-0.0790.010.07480.0498-0.0506-0.02360.13020.01380.02390.2267-0.07550.269950.894563.3736-53.2736
171.3499-0.5134-0.26583.6516-1.24320.5771-0.02910.05520.06810.24460.03750.032-0.0786-0.044-0.00840.1611-0.02370.00110.2522-0.02740.262254.280653.6029-62.3519
180.6941-0.54440.48540.4454-0.41450.9624-0.0914-0.11510.00210.04950.05210.0490.0599-0.12740.03930.1939-0.00620.03990.2428-0.05780.230466.153756.2565-50.8217
190.34040.24350.05660.20570.14251.035-0.04130.02930.0556-0.0101-0.01430.15810.2334-0.23040.05560.107-0.0913-0.0790.08280.02070.601840.951426.3055-66.6504
200.1242-0.25-0.11930.52330.24340.1508-0.0022-0.0385-0.06260.01140.02530.1730.0407-0.0205-0.0230.1756-0.0671-0.03970.20480.03570.328849.109339.7582-64.3914
210.41280.1927-0.06691.1236-0.11921.14140.0443-0.01060.031-0.0910.13030.25650.036-0.0685-0.17460.1947-0.0222-0.05790.1898-0.00910.254756.752935.5755-76.4558
222.3369-0.23791.31360.0684-0.13762.061-0.0805-0.1005-0.1843-0.00940.09590.03630.19540.1769-0.01530.27980.0426-0.0860.2106-0.05310.203875.769220.1539-81.2151
230.25090.1530.25270.15370.14040.54570.04220.0527-0.0429-0.01890.02190.04190.0860.1212-0.06410.21460.0316-0.02680.2687-0.0630.182179.777635.9966-77.0785
240.91550.09580.43390.668-0.51471.19410.0961-0.1054-0.05560.01090.07610.07770.0379-0.0202-0.17220.19720.0216-0.05540.2067-0.03370.205268.275828.5279-65.7331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 115
2X-RAY DIFFRACTION2A116 - 194
3X-RAY DIFFRACTION3A195 - 255
4X-RAY DIFFRACTION4B-4 - 98
5X-RAY DIFFRACTION5B99 - 137
6X-RAY DIFFRACTION6B138 - 255
7X-RAY DIFFRACTION7C-3 - 34
8X-RAY DIFFRACTION8C35 - 114
9X-RAY DIFFRACTION9C115 - 255
10X-RAY DIFFRACTION10D-5 - 7
11X-RAY DIFFRACTION11D8 - 176
12X-RAY DIFFRACTION12D177 - 255
13X-RAY DIFFRACTION13E-1 - 28
14X-RAY DIFFRACTION14E29 - 109
15X-RAY DIFFRACTION15E110 - 255
16X-RAY DIFFRACTION16F-3 - 154
17X-RAY DIFFRACTION17F155 - 184
18X-RAY DIFFRACTION18F185 - 255
19X-RAY DIFFRACTION19G0 - 93
20X-RAY DIFFRACTION20G94 - 207
21X-RAY DIFFRACTION21G208 - 255
22X-RAY DIFFRACTION22H-4 - 55
23X-RAY DIFFRACTION23H56 - 189
24X-RAY DIFFRACTION24H190 - 255

+
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