[English] 日本語
Yorodumi
- PDB-5jzm: Structure of wild type Amidase from Vibrio cholerae 0395 at low t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jzm
TitleStructure of wild type Amidase from Vibrio cholerae 0395 at low temparature at 1.8 Angstroms resolution.
ComponentsIntracellular protease/amidase
KeywordsLYASE / Heat shock protein
Function / homology
Function and homology information


D-lactate dehydratase / glyoxalase III activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / protein deglycase activity / DNA repair / cytoplasm
Similarity search - Function
Protein/nucleic acid deglycase HchA / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-lactate dehydratase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsChowdhury, S.R. / Sen, U.
CitationJournal: To Be Published
Title: Structure of wild type Amidase from Vibrio cholerae 0395 at high temparature at 1.8 Angstroms resolution.
Authors: Chowdhury, S.R. / Sen, U.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Intracellular protease/amidase
B: Intracellular protease/amidase
C: Intracellular protease/amidase
D: Intracellular protease/amidase
E: Intracellular protease/amidase
F: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)189,0696
Polymers189,0696
Non-polymers00
Water30,4631691
1
A: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,5121
Polymers31,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,5121
Polymers31,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,5121
Polymers31,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,5121
Polymers31,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,5121
Polymers31,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,5121
Polymers31,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.920, 79.720, 133.580
Angle α, β, γ (deg.)90.00, 95.04, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Intracellular protease/amidase


Mass: 31511.557 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_0351, VC395_A0912 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3AFW5, D-lactate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1691 / 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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 5% PEG 6000, 0.1M Na-citrate, 8% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→36.313 Å / Num. obs: 118593 / % possible obs: 93.04 % / Redundancy: 1.79 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 1.34
Reflection shellResolution: 1.87→1.96 Å

-
Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N57
Resolution: 1.87→36.313 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.23
RfactorNum. reflection% reflection
Rfree0.196 2000 1.69 %
Rwork0.1583 --
obs0.1589 118593 93.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.87→36.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12984 0 0 1691 14675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01213356
X-RAY DIFFRACTIONf_angle_d1.35218150
X-RAY DIFFRACTIONf_dihedral_angle_d14.2924782
X-RAY DIFFRACTIONf_chiral_restr0.0831902
X-RAY DIFFRACTIONf_plane_restr0.0082400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8714-1.91820.28961280.23637506X-RAY DIFFRACTION85
1.9182-1.97010.27651420.21558248X-RAY DIFFRACTION92
1.9701-2.02810.24691400.19628155X-RAY DIFFRACTION92
2.0281-2.09350.24821410.18218251X-RAY DIFFRACTION92
2.0935-2.16830.23441410.17038180X-RAY DIFFRACTION92
2.1683-2.25510.21741400.16348176X-RAY DIFFRACTION92
2.2551-2.35770.22891420.16388277X-RAY DIFFRACTION93
2.3577-2.4820.19871430.16358367X-RAY DIFFRACTION94
2.482-2.63750.20771460.16468512X-RAY DIFFRACTION95
2.6375-2.84110.19891490.16528662X-RAY DIFFRACTION97
2.8411-3.12680.20951480.16038618X-RAY DIFFRACTION97
3.1268-3.57890.19921480.13838653X-RAY DIFFRACTION96
3.5789-4.50770.11791470.12248590X-RAY DIFFRACTION95
4.5077-36.32010.17271450.15428398X-RAY DIFFRACTION92
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)
13.73930.0857-1.54142.15440.13512.2648-0.07730.2056-0.074-0.0092-0.00780.16760.1845-0.25150.05550.1412-0.02560.00640.1405-0.02360.15-17.9946-11.28015.0933
20.65-0.1691-0.26690.36980.25420.836-0.0137-0.04130.0533-0.00790.017-0.0088-0.05990.0055-0.00690.1311-0.00590.00320.1090.00320.1351-14.26145.162120.8041
32.2006-0.3946-0.10392.06310.11291.0403-0.00450.11620.186-0.1133-0.00040.1808-0.1512-0.08750.01570.1636-0.00910.00980.14280.0040.1368-18.35578.714812.7981
41.3053-0.1554-0.31011.58010.01491.0231-0.0186-0.17140.02650.11380.0023-0.1491-0.05750.13090.00950.1338-0.0131-0.01320.15090.00430.1333-4.88012.968929.7092
50.55190.26680.1720.52060.45491.9013-0.0028-0.039-0.11340.06210.01-0.07090.1764-0.0425-0.03080.1667-00.03090.13030.01880.2065-13.5406-13.200826.7845
61.545-0.45210.51830.7765-0.66752.2441-0.0329-0.1634-0.11530.05850.04210.1090.0640.0013-0.01790.1638-0.00410.00830.150.01030.1629-20.181-4.905833.5211
75.15711.78041.92468.34824.3989.17430.1314-0.35930.0580.2591-0.0094-0.1146-0.2841-0.2036-0.03020.13580.01420.04140.13250.03710.1435-21.19310.228334.2968
82.42990.1958-2.57021.66970.36286.02960.0160.18390.0564-0.2012-0.02480.1489-0.0867-0.2343-0.04140.13960.0132-0.03520.10610.01740.1452-7.52544.5507-6.8071
91.9082-1.0109-0.02911.84180.48261.12990.17440.2588-0.2419-0.0852-0.14320.06090.20370.1895-0.09150.1512-0.02350.01510.1087-0.0050.170217.1158-16.6861-7.0961
100.933-0.2329-0.48560.52390.15110.4796-0.0491-0.1027-0.07630.05320.02560.02560.02180.05470.02180.1324-0.00810.00020.1299-0.00130.12277.7864-5.2723.8237
111.4814-0.5866-0.45212.7602-0.59262.1584-0.05050.0281-0.1896-0.115-0.05560.03310.1683-0.04490.12390.1252-0.0190.00960.1164-0.01430.18383.6313-13.7353-2.7283
128.07020.96260.92073.33540.43184.00180.2204-0.7716-0.18380.4177-0.0581-0.12990.17510.0996-0.12750.2158-0.004-0.01160.1970.02730.120315.9734-9.635318.2518
132.1608-0.67490.33891.6748-0.580.99230.0269-0.1946-0.03180.14310.0208-0.0041-0.03570.0689-0.02450.1055-0.0132-0.00730.11840.00070.075617.5478-0.07558.5961
142.6558-0.54940.2270.4745-0.23060.5197-0.0106-0.12420.21170.04910.0004-0.0616-0.09990.02620.04070.1518-0.01740.01570.1205-0.00050.145512.818110.9501-0.5058
151.5620.21320.47841.05750.08271.08580.06890.02050.0656-0.0632-0.0213-0.04140.03330.0909-0.030.1361-0.00120.0160.12630.0020.137721.83113.2741-4.7159
166.1828-1.68843.23625.1261-2.18756.9320.07110.1767-0.0350.0327-0.0491-0.49610.07210.4776-0.03070.1282-0.01960.02750.1432-0.01450.150525.2253-11.4491-3.0956
173.29790.2573-0.97732.188-0.50482.6135-0.0418-0.1418-0.40550.0122-0.06870.03990.2822-0.1050.1150.2129-0.0116-0.00450.14670.01630.207814.2425-59.195235.5626
180.8283-1.3415-0.36334.87410.08950.24440.04020.0123-0.1778-0.0893-0.06960.633-0.0166-0.06830.03550.1916-0.0123-0.01650.23220.01130.2597-7.7448-35.69836.7795
191.0099-0.2178-0.56450.62490.36270.455-0.0062-0.00110.02050.01520.0140.03230.028-0.0317-0.00940.1379-0.00460.00630.13680.0070.138110.3582-38.644336.8092
202.228-0.1807-0.28484.0643-1.2792.0969-0.0040.2899-0.2106-0.2048-0.01450.15990.1018-0.2160.0120.1417-0.0021-0.01410.1569-0.02840.12962.5671-42.217129.1217
213.09220.55450.77514.28421.49382.70840.0485-0.06670.3295-0.02690.0988-0.012-0.23920.1798-0.14320.1949-0.02410.04190.15350.02070.185814.817-22.128836.9487
220.9439-0.4691-0.02321.7538-0.3080.7619-0.0146-0.05810.0250.129-0.00230.0304-0.06650.04080.0060.1695-0.01010.02080.162-0.01430.141412.599-31.536446.2994
231.3517-0.9719-0.60592.36620.86732.3556-0.0206-0.2362-0.04460.38320.02140.11010.09710.0587-0.00270.1715-0.00340.00780.19440.0250.120812.1544-42.53854.2913
240.8265-0.477-0.44262.5511.25341.0758-0.0686-0.186-0.02530.16070.08460.01460.16890.0301-0.02850.19450.00630.01420.16380.02240.169517.7307-47.928750.8198
251.0330.39250.44681.03160.12141.1677-0.0663-0.10260.04130.010.07610.1501-0.0331-0.0953-0.01120.1590.00730.02950.13850.00590.15323.2709-39.393253.878
263.2778-1.20760.18832.0055-0.32654.37710.0181-0.09680.20930.29880.08540.1814-0.2189-0.2727-0.09160.1513-0.00820.02760.2097-0.00130.1735-5.3353-30.034445.2798
273.75390.05-1.12541.1914-1.07022.894-0.05950.4205-0.3309-0.1704-0.03910.06220.2972-0.27240.14840.1725-0.014-0.02470.1812-0.0480.162518.2949-51.255815.0423
282.4236-0.07790.88751.26530.82731.34250.07690.1221-0.27480.12270.1483-0.26510.12990.2159-0.23740.20570.00650.01470.15370.02180.196548.9779-52.012423.8083
290.5906-0.2-0.32290.56690.08640.19070.0262-0.02550.01110.0088-0.0332-0.01920.02810.0040.0130.12740.0005-0.0010.13530.00550.12633.3604-42.984126.7551
302.2749-1.079-0.01991.0549-0.13330.8647-0.0421-0.1022-0.26960.0877-0.05210.06580.21880.01970.09060.192-0.0180.03060.12780.02020.175135.3475-54.181627.7064
316.8722.13650.82323.06131.052.57850.2668-0.33620.40650.3841-0.20150.0005-0.17070.0503-0.05670.20840.0045-0.0050.17-0.01010.139839.2868-32.738739.2545
321.75820.19090.54120.81290.04371.40130.0505-0.09410.10670.0844-0.0340.0157-0.08270.03770.00830.1393-0.01140.00470.1116-0.00740.130438.1105-31.961525.6868
333.64481.4925-0.47671.1849-0.31880.42190.0320.2210.2345-0.09930.02540.0747-0.0952-0.0994-0.03090.14220.02520.00310.16070.00920.106630.7328-33.008412.5865
340.95420.3494-0.38462.42380.24571.0409-0.00520.0708-0.01640.0184-0.0237-0.09570.076-0.02230.03010.14480.00730.01150.15060.00530.151743.0448-35.883412.7829
354.43892.32921.27896.36242.44566.0415-0.05890.0608-0.0689-0.09180.1266-0.5442-0.16090.5721-0.1030.130.00790.03460.17330.01730.180452.5468-42.287522.6263
364.7208-1.5721-2.39253.03750.21653.58490.2441-0.11370.74410.20740.1841-0.4237-0.64470.1708-0.35370.2936-0.00250.02080.198-0.05990.313615.13718.497463.5253
370.9560.2306-0.15551.4214-0.91942.26030.1546-0.2281-0.17860.7101-0.1271-0.1919-0.0729-0.0365-0.03130.2804-0.0143-0.07660.32390.02380.24178.802-4.90184.874
380.72160.1987-0.14210.9505-0.09690.8514-0.0172-0.0945-0.02880.00820.0025-0.11570.05230.03380.00710.18310.01830.01040.2065-0.00960.168412.2601-1.934567.1995
391.2084-0.38520.02761.7655-1.3632.45150.0385-0.3197-0.04730.2339-0.1885-0.3181-0.1390.2580.10960.223-0.0059-0.05990.3157-0.00510.248418.68831.579676.2744
404.65152.0181-0.89765.6112-0.71774.7983-0.54240.423-0.744-0.10950.2636-0.1350.5012-0.18290.20120.25140.04960.0830.1945-0.02970.319912.0482-18.502962.6863
411.26450.3871-0.25442.6776-0.80661.1273-0.04020.0381-0.1398-0.0416-0.0143-0.06350.1524-0.07230.04710.17760.01290.00910.1823-0.01350.15773.1026-8.489363.307
421.60560.59-0.4561.0416-0.35660.83950.01080.05740.10570.03170.05890.0625-0.0547-0.1303-0.06840.18290.03260.0130.2136-0.00170.167-3.65453.071264.4241
434.34162.53860.03132.00820.57512.43990.2814-0.2025-0.16070.4787-0.2941-0.04980.0442-0.03650.02120.22310.0188-0.00350.29780.00420.12310.7911-9.92780.9833
442.74940.90950.80942.6122-0.48721.24750.0843-0.56420.25450.22080.0301-0.6484-0.51430.5485-0.06590.322-0.0827-0.03410.4084-0.17430.393435.300912.453462.762
452.04631.95622.4782.05572.96865.0523-0.19410.34580.2897-0.40910.23570.0844-0.91610.1162-0.05150.4354-0.04440.02640.32750.11010.436733.53588.537231.1653
462.193-0.0404-0.46261.34890.43720.8544-0.0127-0.00080.2389-0.00960.0329-0.1031-0.00440.0227-0.01450.1331-0.00140.00280.1362-0.0050.16528.08851.065946.9327
473.10370.8156-0.26811.2239-0.31062.27850.30560.48151.0218-0.1344-0.0430.1249-0.4203-0.1282-0.18510.29910.05450.0780.23880.05680.455926.2811.794942.9395
484.1169-0.0034-0.29946.10751.38376.1718-0.18810.3426-0.4061-0.0251-0.05560.34840.3021-0.31360.25240.1278-0.0363-0.00180.1925-0.01070.170118.4931-11.606140.0776
492.22150.20910.12231.34140.27412.5477-0.07580.0241-0.12830.03520.03130.01440.1075-0.07230.0550.1592-0.0090.01790.1534-0.01040.170931.3271-10.079744.1505
501.611-0.5604-0.87641.49270.69872.7593-0.1963-0.46180.03150.09890.0537-0.18440.18030.28720.12420.16070.0286-0.02540.31-0.00190.231242.31-6.495853.8045
511.6458-0.9347-0.78843.28480.08831.164-0.0355-0.02950.2046-0.0234-0.0246-0.22360.05530.11940.04860.1757-0.03120.0080.19230.00880.220144.5564-5.131141.5846
524.67571.17611.99255.16422.08425.6709-0.04720.8830.1816-0.53520.2591-0.0976-0.24060.0296-0.25380.205-0.02870.05470.3470.05920.213736.8143-1.288429.3218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 107 )
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 130 )
4X-RAY DIFFRACTION4chain 'A' and (resid 131 through 197 )
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 240 )
6X-RAY DIFFRACTION6chain 'A' and (resid 241 through 267 )
7X-RAY DIFFRACTION7chain 'A' and (resid 268 through 285 )
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 30 )
9X-RAY DIFFRACTION9chain 'B' and (resid 31 through 50 )
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 107 )
11X-RAY DIFFRACTION11chain 'B' and (resid 108 through 130 )
12X-RAY DIFFRACTION12chain 'B' and (resid 131 through 148 )
13X-RAY DIFFRACTION13chain 'B' and (resid 149 through 197 )
14X-RAY DIFFRACTION14chain 'B' and (resid 198 through 240 )
15X-RAY DIFFRACTION15chain 'B' and (resid 241 through 267 )
16X-RAY DIFFRACTION16chain 'B' and (resid 268 through 285 )
17X-RAY DIFFRACTION17chain 'C' and (resid 5 through 30 )
18X-RAY DIFFRACTION18chain 'C' and (resid 31 through 50 )
19X-RAY DIFFRACTION19chain 'C' and (resid 51 through 107 )
20X-RAY DIFFRACTION20chain 'C' and (resid 108 through 130 )
21X-RAY DIFFRACTION21chain 'C' and (resid 131 through 148 )
22X-RAY DIFFRACTION22chain 'C' and (resid 149 through 197 )
23X-RAY DIFFRACTION23chain 'C' and (resid 198 through 222 )
24X-RAY DIFFRACTION24chain 'C' and (resid 223 through 240 )
25X-RAY DIFFRACTION25chain 'C' and (resid 241 through 267 )
26X-RAY DIFFRACTION26chain 'C' and (resid 268 through 285 )
27X-RAY DIFFRACTION27chain 'D' and (resid 5 through 30 )
28X-RAY DIFFRACTION28chain 'D' and (resid 31 through 50 )
29X-RAY DIFFRACTION29chain 'D' and (resid 51 through 107 )
30X-RAY DIFFRACTION30chain 'D' and (resid 108 through 130 )
31X-RAY DIFFRACTION31chain 'D' and (resid 131 through 148 )
32X-RAY DIFFRACTION32chain 'D' and (resid 149 through 197 )
33X-RAY DIFFRACTION33chain 'D' and (resid 198 through 240 )
34X-RAY DIFFRACTION34chain 'D' and (resid 241 through 267 )
35X-RAY DIFFRACTION35chain 'D' and (resid 268 through 285 )
36X-RAY DIFFRACTION36chain 'E' and (resid 5 through 30 )
37X-RAY DIFFRACTION37chain 'E' and (resid 31 through 50 )
38X-RAY DIFFRACTION38chain 'E' and (resid 51 through 107 )
39X-RAY DIFFRACTION39chain 'E' and (resid 108 through 130 )
40X-RAY DIFFRACTION40chain 'E' and (resid 131 through 148 )
41X-RAY DIFFRACTION41chain 'E' and (resid 149 through 197 )
42X-RAY DIFFRACTION42chain 'E' and (resid 198 through 267 )
43X-RAY DIFFRACTION43chain 'E' and (resid 268 through 285 )
44X-RAY DIFFRACTION44chain 'F' and (resid 5 through 30 )
45X-RAY DIFFRACTION45chain 'F' and (resid 31 through 50 )
46X-RAY DIFFRACTION46chain 'F' and (resid 51 through 107 )
47X-RAY DIFFRACTION47chain 'F' and (resid 108 through 130 )
48X-RAY DIFFRACTION48chain 'F' and (resid 131 through 148 )
49X-RAY DIFFRACTION49chain 'F' and (resid 149 through 197 )
50X-RAY DIFFRACTION50chain 'F' and (resid 198 through 240 )
51X-RAY DIFFRACTION51chain 'F' and (resid 241 through 267 )
52X-RAY DIFFRACTION52chain 'F' and (resid 268 through 285 )

+
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://pdbjlvh1.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