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- PDB-5v6q: Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate r... -

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Basic information

Entry
Database: PDB / ID: 5v6q
TitleCrystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with NADP and malonate
ComponentsNADPH-dependent glyoxylate/hydroxypyruvate reductase
KeywordsOXIDOREDUCTASE / NADPH-dependent glyoxylate/hydroxypyruvate reductase / NADP / NYSGRC / Sinorhizobium meliloti / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / 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
MALONIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsShabalin, I.G. / Handing, K.B. / Miezaniec, A.P. / Gasiorowska, O.A. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094662 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117080 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HG008424 United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.
Authors: Kutner, J. / Shabalin, I.G. / Matelska, D. / Handing, K.B. / Gasiorowska, O. / Sroka, P. / Gorna, M.W. / Ginalski, K. / Wozniak, K. / Minor, W.
History
DepositionMar 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 16, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_ec
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: NADPH-dependent glyoxylate/hydroxypyruvate reductase
B: NADPH-dependent glyoxylate/hydroxypyruvate reductase
C: NADPH-dependent glyoxylate/hydroxypyruvate reductase
D: NADPH-dependent glyoxylate/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,89315
Polymers137,4344
Non-polymers3,45911
Water15,151841
1
A: NADPH-dependent glyoxylate/hydroxypyruvate reductase
B: NADPH-dependent glyoxylate/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4588
Polymers68,7172
Non-polymers1,7416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-70 kcal/mol
Surface area24190 Å2
MethodPISA
2
C: NADPH-dependent glyoxylate/hydroxypyruvate reductase
D: NADPH-dependent glyoxylate/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4357
Polymers68,7172
Non-polymers1,7185
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-60 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.484, 176.484, 135.857
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

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
11ARGARGARGARGAA3 - 3184 - 319
21ARGARGARGARGBB3 - 3184 - 319
12ARGARGALAALAAA3 - 3194 - 320
22ARGARGALAALACC3 - 3194 - 320
13ARGARGILEILEAA3 - 3204 - 321
23ARGARGILEILEDD3 - 3204 - 321
14SERSERARGARGBB2 - 3183 - 319
24SERSERARGARGCC2 - 3183 - 319
15ARGARGARGARGBB3 - 3184 - 319
25ARGARGARGARGDD3 - 3184 - 319
16ARGARGALAALACC3 - 3194 - 320
26ARGARGALAALADD3 - 3194 - 320

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
NADPH-dependent glyoxylate/hydroxypyruvate reductase


Mass: 34358.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: SMc04462 / Plasmid: pSGC-His / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)-RIPL / References: UniProt: Q92LZ4, hydroxypyruvate reductase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 841 / 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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 uL 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 5 mM NADP + 0.2 uL MCSG Suite II condition #20 (1.1 M malonic acid, 0. ...Details: 0.2 uL 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP, 5 mM NADP + 0.2 uL MCSG Suite II condition #20 (1.1 M malonic acid, 0.072 M succinic acid, 0.15 M ammonium citrate tribasic, 0.18 M DL-malic acid, 0.096 M ammonium tartrate dibasic, 0.24 M sodium acetate, 0.3 M sodium formate, pH 7), equilibrated against 1.5 M sodium chloride in a 96-well, 3-drop crystallization plate (Swissci), incubated with 1/50 v/v 1 mg/mL rTEV at 289 K for 3 hours prior to crystallization

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2014 / Details: Beryllium Lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.587
11K, H, -L20.413
ReflectionResolution: 1.95→50 Å / Num. obs: 114355 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.055 / Rrim(I) all: 0.119 / Rsym value: 0.105 / Χ2: 2.144 / Net I/av σ(I): 22.8 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
1.95-1.984.50.6912.1565356530.6860.3660.7840.6910.86898.6
1.98-2.024.50.6150.7230.3260.6980.89998.7
2.02-2.064.50.5180.8010.2730.5870.96798.6
2.06-2.14.60.4350.8590.2280.4931.04398.9
2.1-2.154.60.3650.8890.1910.4131.13699
2.15-2.24.60.3240.9190.1690.3661.24499.3
2.2-2.254.60.3050.9270.1580.3441.35699.5
2.25-2.314.60.2630.9380.1360.2971.40999.7
2.31-2.384.70.2450.9510.1260.2761.49399.8
2.38-2.464.70.2220.960.1140.2511.627100
2.46-2.544.70.1960.9640.10.2211.869100
2.54-2.654.70.1790.9730.0920.2022.003100
2.65-2.774.70.1570.9770.080.1762.352100
2.77-2.914.70.1360.9820.070.1532.799100
2.91-3.14.60.1190.9860.0620.1343.207100
3.1-3.334.60.10.9890.0520.1133.5399.9
3.33-3.674.40.0840.9920.0440.0953.885100
3.67-4.24.40.0720.9940.0380.0824.016100
4.2-5.294.30.0650.9940.0340.0733.919100
5.29-504.40.0570.9960.030.0653.48899.5

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Processing

Software
NameVersionClassification
MD2data collection
HKL-3000data scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5J23
Resolution: 1.95→40.29 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 3.603 / SU ML: 0.061 / SU R Cruickshank DPI: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.02
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1565 5559 4.9 %RANDOM
Rwork0.1438 ---
obs0.1444 108794 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.88 Å2 / Biso mean: 33.875 Å2 / Biso min: 18.25 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å2-0 Å2-0 Å2
2---2.22 Å2-0 Å2
3---4.43 Å2
Refinement stepCycle: final / Resolution: 1.95→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9446 0 223 841 10510
Biso mean--31.46 38.92 -
Num. residues----1274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0199850
X-RAY DIFFRACTIONr_bond_other_d0.0040.029654
X-RAY DIFFRACTIONr_angle_refined_deg1.342.00313492
X-RAY DIFFRACTIONr_angle_other_deg1.1322057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9451270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50722.402358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.866151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.31596
X-RAY DIFFRACTIONr_chiral_restr0.0690.21642
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111030
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022142
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A391020.05
12B391020.05
21A396500.04
22C396500.04
31A392440.04
32D392440.04
41B392320.04
42C392320.04
51B395400.02
52D395400.02
61C393100.04
62D393100.04
LS refinement shellResolution: 1.951→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 422 -
Rwork0.216 7946 -
all-8368 -
obs--98.22 %
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)
11.7409-0.8201-0.16543.8198-0.07182.96040.20940.13240.1828-0.32550.0492-0.2629-0.27730.4067-0.25860.1135-0.07610.12810.1654-0.06730.17167.13282.5737.735
20.830.1240.43251.78680.20492.10720.0141-0.03540.02760.14370.1639-0.1604-0.02180.4622-0.17790.0748-0.03450.07620.2014-0.11080.149567.679.6650.363
30.0490.07370.0071.24260.28170.58250.06670.0042-0.00420.1354-0.04220.00140.0037-0.0077-0.02440.0988-0.02450.01540.131-0.05130.134563.52646.41135.673
42.1421-0.2913-1.312.54211.23774.87860.09460.0745-0.04870.5088-0.12790.77150.1921-0.57940.03340.1537-0.05880.18190.1394-0.0210.281747.83150.23649.265
50.79330.2897-0.4931.94870.03621.512-0.0199-0.1140.00280.64220.031-0.1230.13480.0222-0.01110.2682-0.0042-0.01550.0798-0.0430.048766.52748.75851.228
60.3437-0.7656-0.30972.01830.82540.55150.08590.00680.0656-0.0196-0.0275-0.0528-0.0424-0.0248-0.05840.1284-0.02770.07650.1193-0.04870.155458.86774.85742.478
74.48990.39190.25013.29950.27572.93190.1016-0.2228-0.35230.13480.0132-0.0690.26780.1529-0.11480.09430.0426-0.09060.11990.01030.172562.42913.34526.917
80.36030.45490.23711.45920.4350.29490.06190.0368-0.0839-0.10590.0385-0.08890.00010.0685-0.10040.10180.0045-0.03980.1288-0.04140.129963.18627.00619.092
94.9773.25742.42476.1553-0.08651.878-0.00330.1340.0677-0.2194-0.1585-0.25340.08390.17140.16170.0972-0.0028-0.010.09-0.04670.2380.50258.47338.378
100.20470.20030.45951.87850.39741.3880.0474-0.02470.022-0.1303-0.03810.2319-0.0531-0.1777-0.00930.11140.03490.00070.1531-0.03990.137454.42851.8524.52
111.50960.69740.11023.16050.80111.5651-0.00480.09630.0253-0.3411-0.0130.5176-0.0536-0.15720.01780.1680.0166-0.11460.135-0.02190.130851.26347.09912.497
120.36330.28120.06321.45780.21420.27660.05220.0007-0.0289-0.2369-0.0026-0.0549-0.0380.045-0.04960.11870.0043-0.01460.1225-0.04360.092962.14937.2318.057
135.3342-0.71180.69912.1946-0.70522.76060.10870.2531-0.3237-0.09270.0458-0.00770.0854-0.0079-0.15460.1553-0.0057-0.07120.0434-0.06620.155836.5211.75457.225
140.9406-0.11490.38380.2623-0.05530.16850.0383-0.0633-0.09990.03460.0375-0.01090.0352-0.0337-0.07580.1389-0.005-0.06880.1021-0.01190.137726.1079.24861.779
151.3605-0.46720.71670.29420.07611.4809-0.0657-0.060.12940.04830.0886-0.06-0.11860.0366-0.02290.17750.0184-0.05710.08830.00430.143110.69529.97458.534
164.0819-0.25920.10852.31480.71441.2782-0.1342-0.29860.34490.23080.1872-0.1266-0.06690.048-0.05310.18070.0473-0.07540.1542-0.09110.087217.2633.42470.622
171.279-0.574-0.11251.14910.57040.8723-0.0937-0.3832-0.18790.21570.17470.07360.0061-0.1172-0.08090.13620.0467-0.02580.20080.07370.08878.39218.18469.799
182.1598-0.66320.93320.4014-0.19770.45320.00810.0415-0.04360.02680.0489-0.0447-0.00830.0498-0.05690.1312-0.0006-0.06080.0976-0.03030.134335.25913.60460.88
192.54120.0504-0.13522.3445-0.39392.59870.14-0.11710.02330.1287-0.06960.15360.1153-0.3366-0.07030.0665-0.01590.0360.14470.07070.1569-20.21638.17943.367
200.7093-0.43320.19020.528-0.26130.21950.0730.0959-0.0156-0.01820.00150.0380.0239-0.0192-0.07450.11310.0128-0.01530.11320.04860.1304-6.23132.10538.619
211.1211-0.77460.0581.0008-0.62140.9450.0830.0850.03730.0218-0.0405-0.0363-0.03820.1187-0.04250.099-0.001-0.04690.13250.0130.12616.29723.6446.094
222.1706-0.68950.68392.2408-0.54932.75360.1680.3270.2794-0.0926-0.1465-0.2288-0.10760.1816-0.02160.09520.00980.03630.16780.09290.083315.62533.9931.864
231.0093-0.72970.00111.1653-0.05980.39690.12250.1586-0.0745-0.0609-0.05510.06110.06850.0122-0.06740.11820.0138-0.04190.12070.0220.08982.19727.03436.977
240.04530.3444-0.18433.40260.25934.62580.02330.01010.01460.13750.08730.0132-0.1998-0.1171-0.11060.10240.0160.00850.16230.07330.174-11.85153.19431.128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 24
2X-RAY DIFFRACTION2A25 - 93
3X-RAY DIFFRACTION3A94 - 161
4X-RAY DIFFRACTION4A162 - 187
5X-RAY DIFFRACTION5A188 - 271
6X-RAY DIFFRACTION6A272 - 320
7X-RAY DIFFRACTION7B1 - 26
8X-RAY DIFFRACTION8B27 - 121
9X-RAY DIFFRACTION9B122 - 132
10X-RAY DIFFRACTION10B133 - 170
11X-RAY DIFFRACTION11B171 - 209
12X-RAY DIFFRACTION12B210 - 319
13X-RAY DIFFRACTION13C2 - 18
14X-RAY DIFFRACTION14C19 - 128
15X-RAY DIFFRACTION15C129 - 171
16X-RAY DIFFRACTION16C172 - 200
17X-RAY DIFFRACTION17C201 - 271
18X-RAY DIFFRACTION18C272 - 320
19X-RAY DIFFRACTION19D3 - 33
20X-RAY DIFFRACTION20D34 - 126
21X-RAY DIFFRACTION21D127 - 165
22X-RAY DIFFRACTION22D166 - 209
23X-RAY DIFFRACTION23D210 - 311
24X-RAY DIFFRACTION24D312 - 320

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