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- PDB-4zfj: Ergothioneine-biosynthetic Ntn hydrolase EgtC, apo form -

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Basic information

Entry
Database: PDB / ID: 4zfj
TitleErgothioneine-biosynthetic Ntn hydrolase EgtC, apo form
ComponentsAmidohydrolase EgtC
KeywordsHYDROLASE / Ntn hydrolase / ergothioneine biosynthesis / sulfur chemistry / Mycobacteria
Function / homology
Function and homology information


gamma-glutamyl hercynylcysteine S-oxide hydrolase / ergothioneine biosynthesis from histidine via gamma-glutamyl-hercynylcysteine sulfoxide / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / glutamine metabolic process
Similarity search - Function
Ergothioneine biosynthesis protein EgtC / Gamma-glutamyl-hercynylcysteine sulfoxide hydrolase, Actinobacteria / Gamma-glutamyl-hercynylcysteine sulfoxide hydrolase EgtC-like / Glutamine amidotransferases class-II / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal ...Ergothioneine biosynthesis protein EgtC / Gamma-glutamyl-hercynylcysteine sulfoxide hydrolase, Actinobacteria / Gamma-glutamyl-hercynylcysteine sulfoxide hydrolase EgtC-like / Glutamine amidotransferases class-II / Glutamine amidotransferase domain / Glutamine amidotransferase type 2 domain profile. / Glutamine amidotransferase type 2 domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Gamma-glutamyl-hercynylcysteine sulfoxide hydrolase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsVit, A. / Seebeck, F.P. / Blankenfeldt, W.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation147005 Switzerland
CitationJournal: Chembiochem / Year: 2015
Title: Structure of the Ergothioneine-Biosynthesis Amidohydrolase EgtC.
Authors: Vit, A. / Mashabela, G.T. / Blankenfeldt, W. / Seebeck, F.P.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support
Item: _diffrn_radiation_wavelength.wavelength / _pdbx_audit_support.funding_organization
Revision 1.3Oct 18, 2017Group: Data collection / Category: diffrn_radiation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amidohydrolase EgtC
B: Amidohydrolase EgtC
C: Amidohydrolase EgtC
D: Amidohydrolase EgtC
E: Amidohydrolase EgtC
F: Amidohydrolase EgtC
G: Amidohydrolase EgtC
H: Amidohydrolase EgtC
I: Amidohydrolase EgtC
J: Amidohydrolase EgtC
K: Amidohydrolase EgtC
L: Amidohydrolase EgtC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,49435
Polymers303,10812
Non-polymers7,38723
Water44,6952481
1
A: Amidohydrolase EgtC
B: Amidohydrolase EgtC
C: Amidohydrolase EgtC
D: Amidohydrolase EgtC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,65112
Polymers101,0364
Non-polymers2,6158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: Amidohydrolase EgtC
H: Amidohydrolase EgtC
J: Amidohydrolase EgtC
K: Amidohydrolase EgtC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,65112
Polymers101,0364
Non-polymers2,6158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
F: Amidohydrolase EgtC
G: Amidohydrolase EgtC
I: Amidohydrolase EgtC
L: Amidohydrolase EgtC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,19211
Polymers101,0364
Non-polymers2,1577
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.977, 69.507, 160.375
Angle α, β, γ (deg.)90.00, 94.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Amidohydrolase EgtC


Mass: 25258.975 Da / Num. of mol.: 12 / Mutation: E53D, L84V, P95S, D118A, V137L, H188R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: egtC, MSMEG_6248, MSMEI_6087 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0R5M9, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL / Polyethylene glycol


Mass: 458.541 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2481 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.4, 10-12% PEG 20000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.9786
SYNCHROTRONSLS X10SA20.9792
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELOct 6, 2010
DECTRIS PILATUS 6M2PIXELAug 22, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2double crystal Si(111)SINGLE WAVELENGTHMx-ray2
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97921
ReflectionRedundancy: 13.7 % / Number: 3248829 / Rmerge(I) obs: 0.138 / D res high: 1.85 Å / D res low: 47.83 Å / Num. obs: 236707 / % possible obs: 98.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
1.851.8811.07714
10.1347.8310.05813.4
ReflectionResolution: 1.75→47.64 Å / Num. obs: 283662 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.047 / Net I/σ(I): 10.3 / Num. measured all: 958644
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 % / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.75-1.780.6541.947488140380.6970.41599.8
9.59-47.640.02824.9622918510.9990.01798.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.2data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→47.641 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 17.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1801 13870 4.89 %
Rwork0.1494 --
obs0.1509 283575 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→47.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20316 0 419 2481 23216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621375
X-RAY DIFFRACTIONf_angle_d1.17629171
X-RAY DIFFRACTIONf_dihedral_angle_d13.6047656
X-RAY DIFFRACTIONf_chiral_restr0.043269
X-RAY DIFFRACTIONf_plane_restr0.0053800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.25774860.22868996X-RAY DIFFRACTION100
1.7699-1.79070.24544770.21928942X-RAY DIFFRACTION100
1.7907-1.81260.2574130.21089009X-RAY DIFFRACTION100
1.8126-1.83550.23234280.20818999X-RAY DIFFRACTION100
1.8355-1.85970.25894710.20418940X-RAY DIFFRACTION100
1.8597-1.88510.23164670.19728982X-RAY DIFFRACTION100
1.8851-1.91210.22484470.19028944X-RAY DIFFRACTION100
1.9121-1.94060.21484420.17429013X-RAY DIFFRACTION100
1.9406-1.97090.20814680.16888965X-RAY DIFFRACTION100
1.9709-2.00320.20394710.16418995X-RAY DIFFRACTION100
2.0032-2.03780.19724230.16359041X-RAY DIFFRACTION100
2.0378-2.07480.20364650.15798936X-RAY DIFFRACTION100
2.0748-2.11470.19744800.15139030X-RAY DIFFRACTION100
2.1147-2.15790.18015030.14328946X-RAY DIFFRACTION100
2.1579-2.20480.17834630.1468927X-RAY DIFFRACTION100
2.2048-2.25610.18184950.14249001X-RAY DIFFRACTION100
2.2561-2.31250.17774390.14278971X-RAY DIFFRACTION100
2.3125-2.37510.18384910.14458944X-RAY DIFFRACTION99
2.3751-2.4450.19314510.1418944X-RAY DIFFRACTION100
2.445-2.52390.18584400.14689098X-RAY DIFFRACTION100
2.5239-2.61410.18344480.14318988X-RAY DIFFRACTION100
2.6141-2.71870.17774550.13969025X-RAY DIFFRACTION100
2.7187-2.84240.18264610.14238962X-RAY DIFFRACTION99
2.8424-2.99230.17654790.15259025X-RAY DIFFRACTION99
2.9923-3.17970.17924670.15278996X-RAY DIFFRACTION99
3.1797-3.42520.17424740.1438889X-RAY DIFFRACTION98
3.4252-3.76970.15284720.13458921X-RAY DIFFRACTION98
3.7697-4.31490.13854750.12119049X-RAY DIFFRACTION99
4.3149-5.43510.13574470.1189042X-RAY DIFFRACTION98
5.4351-47.65850.18574720.16289185X-RAY DIFFRACTION98
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)
11.20940.02540.27171.17330.18031.62120.0055-0.018-0.00160.00080.0004-0.05610.08910.0296-0.01110.1065-0.0054-0.00720.0632-0.00490.113860.611710.6048121.8137
20.9619-0.33710.26732.0462-0.10432.55310.02980.05410.1546-0.1092-0.0326-0.1475-0.27960.1367-0.01120.136-0.02220.00340.08220.0170.138859.384623.4835108.369
31.7252-0.4813-0.34092.4353-0.77172.0705-0.00740.147-0.068-0.2067-0.0104-0.01450.26280.0127-0.00060.1521-0.0075-0.01460.0806-0.03380.107958.93415.1316106.2273
41.6201-0.1508-0.18871.6443-0.36251.7292-0.0385-0.06460.06890.13490.00540.0052-0.04310.00280.02920.1161-0.0097-0.00040.0641-0.00750.113765.9543.9829135.6581
51.1897-0.45370.72371.8350.07522.25030.03430.0312-0.082-0.0422-0.08020.14270.1056-0.08740.03940.1091-0.02090.00130.0791-0.00820.134156.653545.0784119.4947
61.3082-0.43540.22651.7457-0.10671.9296-0.1002-0.03360.19450.13930.0253-0.0161-0.3211-0.00670.04530.1808-0.0224-0.0240.0613-0.01180.160660.672959.0107131.3247
71.577-0.2720.41841.25620.07361.7835-0.03630.0720.0192-0.0175-0.0217-0.0789-0.05810.11160.04430.0752-0.0213-0.00830.10650.00760.105283.455627.4291131.7645
82.8334-0.72510.37761.642-0.59982.7901-0.0333-0.085-0.23460.01760.0460.07240.3768-0.121-0.01780.1359-0.02470.01010.11460.00990.122283.065316.4586146.8104
91.936-0.0578-0.07071.5017-0.09682.9132-0.05420.1304-0.0087-0.019-0.0455-0.22150.08940.4850.08250.0754-0.00080.00220.21110.01340.171498.077722.7488137.7117
102.04080.15440.13271.76740.0312.07120.0941-0.21020.07260.0713-0.10680.06060.0959-0.2530.0120.1003-0.0510.01530.1484-0.00670.109148.627719.4903140.8157
112.9499-0.67091.04440.1717-0.45773.34230.0585-0.51460.15010.0554-0.0785-0.07280.0418-0.0963-0.00730.153-0.0733-0.00670.2469-0.02590.14759.827616.5816155.227
122.13950.0062-0.42661.2122-0.01481.01180.078-0.52480.05730.3324-0.10960.21560.1762-0.5957-0.0580.1883-0.20540.05220.5132-0.03830.182740.923415.0001154.535
131.4626-0.11950.78641.86350.07521.58890.01080.1210.1449-0.0375-0.133-0.1532-0.07160.1454-0.08320.0939-0.0080.01750.18360.05070.147328.732938.59564.4858
142.20780.00870.70012.2255-0.7850.984-0.0006-0.15980.12380.0678-0.05130.1294-0.0735-0.0136-0.0420.10680.00370.02210.1776-0.02350.159310.181737.891262.8479
152.27410.0718-0.39842.89170.38771.24170.02650.3940.3831-0.1703-0.1476-0.0389-0.13180.1401-0.02890.1903-0.00080.00740.24320.10140.209222.059748.319452.7757
161.59880.18450.07671.362-0.49381.79180.0489-0.18110.21190.035-0.08970.12790.0046-0.2226-0.0470.0962-0.02350.01370.1583-0.03260.1536113.761352.1592140.6725
172.4492-0.18830.89160.19140.07632.65770.1055-0.3890.14550.1174-0.1217-0.00340.1007-0.1985-0.08270.171-0.0703-0.00230.2102-0.03020.1651125.26749.2453155.0063
181.57010.4293-0.09641.38550.73111.00230.3416-0.60690.08870.3683-0.29440.27130.3582-0.3855-0.16370.196-0.17360.06940.4802-0.08180.2133107.040945.7259154.6983
191.5446-0.11640.20441.00630.01871.9506-0.04180.10940.0891-0.0211-0.0562-0.1042-0.0560.14220.00180.1071-0.0278-0.02320.13090.02210.1345147.78863.5145132.001
202.4718-0.79150.10221.7463-0.95962.5039-0.0721-0.0559-0.12290.00220.05670.0220.263-0.00470.03460.1598-0.0213-0.0130.1423-0.00250.1321148.490752.2249146.7148
211.8224-0.38190.76882.4403-0.7153.3989-0.16510.25610.14710.1074-0.1955-0.371-0.16210.76980.16630.1258-0.0404-0.00630.34850.08130.2877163.826960.6308136.4652
222.22190.09340.05771.7106-0.08721.10810.0915-0.1095-0.01940.0312-0.1021-0.03520.0522-0.07280.01990.0842-0.02170.01280.1537-0.0010.094914.703517.523991.0641
231.28750.30881.2571.8585-0.37362.1670.05280.0355-0.0135-0.1837-0.05790.01860.1156-0.03250.0120.1141-0.00560.0190.189-0.01960.12122.505518.926877.0629
242.32650.01960.21212.0989-0.57651.54090.0773-0.2064-0.24750.101-0.03590.06280.2735-0.2992-0.01740.1811-0.0920.0230.24010.02010.15951.31288.474692.8543
252.2670.05650.6331.28370.15852.22850.05760.056-0.0369-0.0542-0.0082-0.00110.13750.037-0.04550.12540.0012-0.00880.0736-0.01470.0975126.371345.3984121.2757
261.1031-0.36850.78832.30770.03913.7219-0.03060.08860.1882-0.0788-0.0054-0.1423-0.30310.20010.02380.1338-0.0133-0.00720.11410.00660.1546123.928858.7117108.4911
272.3674-1.25080.38612.3723-0.26333.01410.11110.1997-0.1484-0.171-0.046-0.00420.49430.1706-0.04510.23110.0136-0.02350.1304-0.05730.1502125.293940.14105.8242
281.7253-0.51750.37671.38690.10510.85810.11770.24530.0321-0.0865-0.1276-0.03420.07130.1462-0.12950.11840.040.03180.2181-0.00860.118835.591716.17269.0636
290.9054-0.14370.96862.15130.06351.30780.05950.09330.05680.0832-0.066-0.13660.08280.1207-0.04760.12810.00240.01740.19680.00410.138349.210217.332182.5546
301.1223-0.0859-0.01922.0776-0.10531.4970.1470.3281-0.174-0.1239-0.1381-0.12420.16670.2868-0.19250.20240.10560.03170.3119-0.04170.185748.23536.154268.0367
311.8711-0.36170.79272.204-0.07522.3267-0.031-0.10760.22560.0053-0.0730.0325-0.0662-0.09730.07070.07720.0017-0.0050.1377-0.04470.142423.171239.736794.4143
323.45540.18790.68892.38851.03663.0757-0.01350.0740.2061-0.01330.0121-0.1593-0.06210.12370.00440.0866-0.0026-0.01370.11310.00520.148642.036838.093697.5312
332.2762-0.75620.30752.11180.29011.4817-0.1094-0.39640.54750.22-0.0256-0.0472-0.1584-0.14270.10010.19660.0112-0.02150.229-0.12340.276430.200749.5459105.786
341.195-0.38210.21942.2558-0.24932.4762-0.1046-0.06230.1170.225-0.04870.0184-0.2006-0.04320.12750.18720.0075-0.03270.0845-0.03070.164128.848178.2758136.9351
352.1228-0.30611.38522.54020.80483.7196-0.1355-0.10710.1972-0.1671-0.14080.3051-0.2581-0.35920.21370.19290.0219-0.04640.148-0.04150.2033119.170479.4603121.0447
361.3683-0.6247-0.17981.79550.53942.0199-0.2125-0.01140.14830.1194-0.1770.2086-0.6779-0.33690.19890.39970.0841-0.09720.166-0.09190.3163122.026392.9279133.7743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 170 )
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 230 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 89 )
5X-RAY DIFFRACTION5chain 'B' and (resid 90 through 170 )
6X-RAY DIFFRACTION6chain 'B' and (resid 171 through 229 )
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 89 )
8X-RAY DIFFRACTION8chain 'C' and (resid 90 through 170 )
9X-RAY DIFFRACTION9chain 'C' and (resid 171 through 230 )
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 89 )
11X-RAY DIFFRACTION11chain 'D' and (resid 90 through 170 )
12X-RAY DIFFRACTION12chain 'D' and (resid 171 through 228 )
13X-RAY DIFFRACTION13chain 'E' and (resid 2 through 89 )
14X-RAY DIFFRACTION14chain 'E' and (resid 90 through 170 )
15X-RAY DIFFRACTION15chain 'E' and (resid 171 through 229 )
16X-RAY DIFFRACTION16chain 'F' and (resid 2 through 89 )
17X-RAY DIFFRACTION17chain 'F' and (resid 90 through 170 )
18X-RAY DIFFRACTION18chain 'F' and (resid 171 through 231 )
19X-RAY DIFFRACTION19chain 'G' and (resid 2 through 89 )
20X-RAY DIFFRACTION20chain 'G' and (resid 90 through 170 )
21X-RAY DIFFRACTION21chain 'G' and (resid 190 through 228 )
22X-RAY DIFFRACTION22chain 'H' and (resid 2 through 89 )
23X-RAY DIFFRACTION23chain 'H' and (resid 90 through 170 )
24X-RAY DIFFRACTION24chain 'H' and (resid 171 through 227 )
25X-RAY DIFFRACTION25chain 'I' and (resid 2 through 89 )
26X-RAY DIFFRACTION26chain 'I' and (resid 90 through 170 )
27X-RAY DIFFRACTION27chain 'I' and (resid 171 through 229 )
28X-RAY DIFFRACTION28chain 'J' and (resid 2 through 89 )
29X-RAY DIFFRACTION29chain 'J' and (resid 98 through 170 )
30X-RAY DIFFRACTION30chain 'J' and (resid 171 through 227 )
31X-RAY DIFFRACTION31chain 'K' and (resid 2 through 89 )
32X-RAY DIFFRACTION32chain 'K' and (resid 98 through 170 )
33X-RAY DIFFRACTION33chain 'K' and (resid 171 through 228 )
34X-RAY DIFFRACTION34chain 'L' and (resid 2 through 89 )
35X-RAY DIFFRACTION35chain 'L' and (resid 90 through 170 )
36X-RAY DIFFRACTION36chain 'L' and (resid 171 through 228 )

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