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- PDB-4olq: Crystal Structure of a Putative enoyl-CoA hydratase/isomerase fam... -

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Basic information

Entry
Database: PDB / ID: 4olq
TitleCrystal Structure of a Putative enoyl-CoA hydratase/isomerase family protein from Hyphomonas neptunium
ComponentsEnoyl-CoA hydratase/isomerase family protein
KeywordsLYASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / enoyl-CoA hydratase / isomerase
Function / homology
Function and homology information


Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
D-MALATE / DI(HYDROXYETHYL)ETHER / Unknown ligand / Enoyl-CoA hydratase/isomerase family protein
Similarity search - Component
Biological speciesHyphomonas neptunium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsSzlachta, K. / Cooper, D.R. / Chapman, H.C. / Cymborowski, M.T. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. ...Szlachta, K. / Cooper, D.R. / Chapman, H.C. / Cymborowski, M.T. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of a Putative enoyl-CoA hydratase/isomerase family protein from Hyphomonas neptunium
Authors: Szlachta, K. / Cooper, D.R. / Chapman, H.C. / Cymborowski, M.T. / Stead, M. / Hillerich, B. / Ahmed, M. / Bonanno, J.B. / Seidel, R. / Almo, S.C. / Minor, W.
History
DepositionJan 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein
C: Enoyl-CoA hydratase/isomerase family protein
D: Enoyl-CoA hydratase/isomerase family protein
E: Enoyl-CoA hydratase/isomerase family protein
F: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,59520
Polymers181,4016
Non-polymers1,19314
Water1,00956
1
A: Enoyl-CoA hydratase/isomerase family protein
B: Enoyl-CoA hydratase/isomerase family protein
C: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3119
Polymers90,7013
Non-polymers6116
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-88 kcal/mol
Surface area29600 Å2
MethodPISA
2
D: Enoyl-CoA hydratase/isomerase family protein
E: Enoyl-CoA hydratase/isomerase family protein
F: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,28311
Polymers90,7013
Non-polymers5838
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-81 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.595, 122.390, 210.232
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A0 - 259
2010B0 - 259
1020A3 - 259
2020C3 - 259
1030A-11 - 260
2030D-11 - 260
1040A-11 - 260
2040E-11 - 260
1050A-1 - 259
2050F-1 - 259
1060B3 - 259
2060C3 - 259
1070B0 - 259
2070D0 - 259
1080B0 - 259
2080E0 - 259
1090B0 - 259
2090F0 - 259
10100C3 - 259
20100D3 - 259
10110C3 - 259
20110E3 - 259
10120C3 - 259
20120F3 - 259
10130D-11 - 260
20130E-11 - 260
10140D-1 - 259
20140F-1 - 259
10150E-1 - 259
20150F-1 - 259

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Detailstwo trimers are in the asymmetric unit

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Enoyl-CoA hydratase/isomerase family protein


Mass: 30233.537 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyphomonas neptunium (bacteria) / Strain: ATCC 15444 / Gene: HNE_1107 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q0C365, enoyl-CoA hydratase

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Non-polymers , 6 types, 70 molecules

#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 8 / Source method: obtained synthetically
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15 M Malic acid, 20% w/v PEG 3350, equilibrated against 1.5 M NaCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2013 / Details: beryllium lenses
RadiationMonochromator: diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 52687 / % possible obs: 99.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.142 / Χ2: 2.111 / Net I/σ(I): 5.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.56-2.64.40.9525500.769196.5
2.6-2.654.725341.096198.8
2.65-2.74.90.81525657.821198.1
2.7-2.765.10.81125790.754199.1
2.76-2.825.10.66725920.751199.3
2.82-2.885.30.62925820.772199.3
2.88-2.965.20.49526140.822199.7
2.96-3.045.30.44726020.873199.7
3.04-3.125.30.37126420.89199.8
3.12-3.235.40.2825770.959199.9
3.23-3.345.40.22526491.0411100
3.34-3.475.40.28126332.4271100
3.47-3.635.50.15726301.3151100
3.63-3.825.50.18226382.3781100
3.82-4.065.40.15926572.7591100
4.06-4.385.40.08526661.959199.8
4.38-4.825.40.07926662.297199.9
4.82-5.515.40.08526902.327199.9
5.51-6.945.30.07727422.3551100
6.94-5050.05428797.77199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
MD2data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2329 / WRfactor Rwork: 0.2026 / FOM work R set: 0.688 / SU B: 40.798 / SU ML: 0.36 / SU Rfree: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 2282 5.1 %RANDOM
Rwork0.23 ---
obs0.2316 45118 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.61 Å2 / Biso mean: 14.735 Å2 / Biso min: 2.01 Å2
Baniso -1Baniso -2Baniso -3
1--4.14 Å20 Å20 Å2
2--0.15 Å20 Å2
3---4 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11456 0 73 56 11585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911717
X-RAY DIFFRACTIONr_bond_other_d0.0070.0211318
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.96915901
X-RAY DIFFRACTIONr_angle_other_deg1.258325896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61551591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2723.65400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.953151741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.31574
X-RAY DIFFRACTIONr_chiral_restr0.0750.21856
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113462
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022518
X-RAY DIFFRACTIONr_mcbond_it0.8131.4476382
X-RAY DIFFRACTIONr_mcbond_other0.8131.4476381
X-RAY DIFFRACTIONr_mcangle_it1.3782.177967
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A138350.08
12B138350.08
21A137110.09
22C137110.09
31A148640.05
32D148640.05
41A145580.09
42E145580.09
51A136190.09
52F136190.09
61B138300.08
62C138300.08
71B139290.08
72D139290.08
81B142730.06
82E142730.06
91B136550.08
92F136550.08
101C138450.09
102D138450.09
111C140620.09
112E140620.09
121C142410.06
122F142410.06
131D145540.09
132E145540.09
141D137080.09
142F137080.09
151E139810.08
152F139810.08
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 171 -
Rwork0.348 3081 -
all-3252 -
obs--99.21 %
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)
125.75146.7362-0.84684.02921.17110.89110.01340.7873-0.35940.4936-0.15230.09810.2323-0.24460.13880.7098-0.0271-0.03891.00520.0180.158419.078-24.581.016
21.63050.0036-0.40842.02780.66991.1780.0070.1129-0.0723-0.08780.0797-0.1244-0.01440.2275-0.08680.2871-0.00330.02791.03460.00280.0186-3.046-25.711.617
32.01211.02691.02761.94250.38511.49440.05490.0660.14960.0142-0.08110.0886-0.16620.15260.02630.2750.0270.02730.91650.01270.0214-12.818-17.03315.629
44.99421.6628-0.35277.2676-6.043813.74170.53370.2106-0.31431.03630.123-0.6148-0.0770.2467-0.65660.40780.1394-0.1250.8845-0.12830.276-3.553-10.66336.074
55.3349-7.1113-2.344924.97674.52411.61510.45390.34570.3686-1.0522-0.451-0.1394-0.2165-0.0601-0.00290.2421-0.15660.01650.75440.13770.27491.2395.83825.863
638.881829.257847.769622.050135.961158.7025-0.0734-0.38630.2939-0.113-0.40210.4141-0.0608-0.51510.47550.64010.074-0.19331.1068-0.17441.4806-52.548-40.84224.966
73.0232-0.1992-0.89443.334-0.94093.3198-0.26830.1122-0.5336-0.08250.13040.26790.2923-0.38760.13780.36-0.10780.02730.88410.0440.1531-45.138-37.40624.933
81.3840.3196-0.70050.30040.01971.4569-0.2678-0.0972-0.2974-0.00720.11080.0320.0312-0.16290.1570.4369-0.05460.03931.06410.05010.1304-40.648-30.94528.315
90.80630.69440.32170.7408-0.42753.8219-0.0644-0.02690.0070.01480.04090.0027-0.23810.0060.02360.2897-0.0098-0.00120.90850.00910.0038-35.088-18.23928.969
103.8792-1.11630.56141.1158-0.62061.2457-0.23090.048-0.4839-0.135-0.0435-0.06070.01660.11370.27440.3628-0.01330.07990.85740.06570.172-21.347-39.09316.318
114.39092.2337-0.73342.7594-0.11251.06030.2131-0.05350.1441-0.0649-0.0289-0.003-0.4593-0.0529-0.18430.39340.00270.03720.7576-0.03870.0553-26.1435.34542.966
126.44673.12874.59741.62941.80516.5370.10610.7857-0.53260.2270.2154-0.3008-0.29910.8284-0.32150.5306-0.0159-0.04151.0502-0.0430.2148-11.7241.28541.784
131.92640.3006-0.84111.2944-0.45620.9416-0.00820.35170.1333-0.03330.0347-0.0131-0.1302-0.1893-0.02650.4035-0.025-0.0471.00710.01060.0161-23.583-3.98130.329
148.04772.7535-4.17887.4733-5.542911.53010.3891-0.88560.03060.1192-0.1428-0.0207-0.0770.6319-0.24640.2345-0.0097-0.05640.7532-0.00860.0305-29.009-23.10644.156
1518.74843.12422.56771.67641.35093.6354-0.0684-0.6995-0.0910.0604-0.18350.4937-0.2181-0.3350.25180.29030.03210.05370.85040.00310.2376-50.097-15.8447.125
163.1839-0.2008-1.76680.03490.24622.01940.1522-0.53640.0915-0.0012-0.051-0.0014-0.02590.2148-0.10120.3705-0.05810.05291.291-0.11810.1667-56.229-22.508100.561
172.98790.86410.0315.1574-0.23410.05830.095-0.2485-0.0768-0.0996-0.08920.17450.0497-0.203-0.00580.2629-0.01870.02721.1587-0.02530.0241-46.455-29.294.016
182.9391-0.33460.28771.93470.16770.23560.0494-0.18830.21460.1483-0.1294-0.130.0324-0.16370.07990.3502-0.02030.01041.2138-0.08760.0492-34.29-23.2591.423
194.74231.15731.21133.9943.18148.5057-0.1305-0.08960.1554-0.02350.1840.42710.6297-0.3579-0.05360.29470.0215-0.12780.87010.020.125-42.449-13.02374.406
204.8813-0.6996-4.996110.62995.4448.36360.019-0.09720.8357-0.48290.60830.369-0.37830.0386-0.62730.19750.1292-0.16490.9563-0.0650.3632-48.70.34174.066
216.2477-8.00895.279312.6159-12.091316.55490.19840.5120.1323-0.3556-0.6549-0.29940.48190.3790.45660.43690.03750.00630.9085-0.06680.25279.615-48.96985.428
222.832-0.0647-1.31630.35480.71871.9692-0.1416-0.0431-0.438-0.03180.0213-0.03740.0053-0.05240.12040.37130.05010.02921.0653-0.06620.0797-2.193-36.02977.152
230.4844-0.3257-0.65111.5854-0.69221.8637-0.0289-0.018-0.04680.0011-0.00760.05730.02680.26130.03650.30550.0186-0.01681.116-0.05240.0105-10.099-23.90478.003
243.66351.31481.98291.90631.69542.29530.1152-0.0163-0.1838-0.1097-0.29910.050.2104-0.12780.18380.4258-0.00730.04451.0512-0.08260.1078-25.91-38.4184.444
258.9467-2.0854-2.81047.6526-3.35494.415-0.3771-1.0384-1.20710.66870.01330.90260.63150.38290.36380.6492-0.06520.27081.034-0.0250.391-29.376-47.15799.032
267.201142.16610.1858247.6631.13240.04210.149-0.12041.1177-0.1387-0.33226.5375-0.07670.10650.18321.464-0.0656-0.19362.1332-0.09410.9681-23.39516.2859.657
276.449-2.1966-1.44113.06361.5572.5275-0.0843-0.15860.34580.1265-0.0311-0.0351-0.26830.11250.11550.40580.0172-0.04510.7111-0.08260.0517-21.1035.01463.116
2862.790332.337919.355623.083214.367316.6543-0.2937-3.6303-0.5219-0.734-0.41270.09391.1537-0.88930.70630.61850.08330.07031.30050.04260.1658-41.5966.74865.971
292.69060.70470.09520.35720.16771.4621-0.1716-0.32080.2076-0.04960.06270.0827-0.1244-0.01680.1090.36580.0832-0.03921.0093-0.11330.0389-27.391-3.61473.522
305.96742.3071-0.30572.8134-1.14552.84880.02870.2046-0.0094-0.0483-0.0117-0.1141-0.0762-0.0284-0.01690.28640.0251-0.01660.8479-0.08260.0202-7.806-17.94259.911
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-11 - 2
2X-RAY DIFFRACTION2A3 - 145
3X-RAY DIFFRACTION3A146 - 213
4X-RAY DIFFRACTION4A214 - 244
5X-RAY DIFFRACTION5A245 - 260
6X-RAY DIFFRACTION6B0 - 5
7X-RAY DIFFRACTION7B6 - 42
8X-RAY DIFFRACTION8B43 - 135
9X-RAY DIFFRACTION9B136 - 184
10X-RAY DIFFRACTION10B185 - 260
11X-RAY DIFFRACTION11C2 - 56
12X-RAY DIFFRACTION12C57 - 98
13X-RAY DIFFRACTION13C99 - 212
14X-RAY DIFFRACTION14C213 - 236
15X-RAY DIFFRACTION15C237 - 260
16X-RAY DIFFRACTION16D-11 - 23
17X-RAY DIFFRACTION17D24 - 83
18X-RAY DIFFRACTION18D84 - 197
19X-RAY DIFFRACTION19D198 - 230
20X-RAY DIFFRACTION20D231 - 260
21X-RAY DIFFRACTION21E-11 - 4
22X-RAY DIFFRACTION22E5 - 83
23X-RAY DIFFRACTION23E84 - 190
24X-RAY DIFFRACTION24E191 - 240
25X-RAY DIFFRACTION25E241 - 260
26X-RAY DIFFRACTION26F-1 - 4
27X-RAY DIFFRACTION27F5 - 62
28X-RAY DIFFRACTION28F63 - 75
29X-RAY DIFFRACTION29F76 - 198
30X-RAY DIFFRACTION30F199 - 260

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