[English] 日本語
Yorodumi
- PDB-5cw2: Crystal structure of Epoxide Hydrolase A from Mycobacterium therm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cw2
TitleCrystal structure of Epoxide Hydrolase A from Mycobacterium thermoresistibile
ComponentsPutative epoxide hydrolase EPHA
KeywordsHYDROLASE / Epoxide hydrolase / 1 / 3-diphenylurea Mycobacterium alpha/beta
Function / homology
Function and homology information


Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,3-DIPHENYLUREA / Putative epoxide hydrolase EPHA
Similarity search - Component
Biological speciesMycobacterium thermoresistibile ATCC 19527 (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchulz, E.C. / Wilmanns, M.
CitationJournal: To Be Published
Title: The crystal structure of mycobacterial Epoxide Hydrolase A
Authors: Schulz, E.C. / Wilmanns, M. / Henderson, S. / Southall, S.
History
DepositionJul 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Putative epoxide hydrolase EPHA
A: Putative epoxide hydrolase EPHA
B: Putative epoxide hydrolase EPHA
D: Putative epoxide hydrolase EPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,1849
Polymers142,3124
Non-polymers8725
Water7,350408
1
C: Putative epoxide hydrolase EPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7902
Polymers35,5781
Non-polymers2121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Putative epoxide hydrolase EPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7902
Polymers35,5781
Non-polymers2121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Putative epoxide hydrolase EPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7902
Polymers35,5781
Non-polymers2121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative epoxide hydrolase EPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8133
Polymers35,5781
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.800, 105.010, 108.950
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Putative epoxide hydrolase EPHA


Mass: 35578.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile ATCC 19527 (unknown)
Gene: KEK_07967 / Production host: Escherichia coli BL21(DE3) (unknown) / Variant (production host): Rosetta II / References: UniProt: G7CF24, epoxide hydrolase
#2: Chemical
ChemComp-BSU / 1,3-DIPHENYLUREA / DIPHENYLCARBAMIDE / 1,3-Diphenylurea


Mass: 212.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H12N2O / Comment: hormone*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M BisTris pH 7.5, 2.15 M (NH4)2SO4, 4.5% (v/v) PEG 400, 1-3% (v/v) 2,3-butanediol

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: MASSIF automated DC
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9752 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9752 Å / Relative weight: 1
ReflectionResolution: 2→47.82 Å / Num. obs: 93380 / % possible obs: 99.47 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.1145 / Net I/σ(I): 7.68
Reflection shellResolution: 2→2.071 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5224 / Mean I/σ(I) obs: 2.42 / % possible all: 99.66

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.819 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.23 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2508 4703 5.04 %
Rwork0.2086 --
obs0.2129 93380 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→47.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9892 0 65 408 10365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01410239
X-RAY DIFFRACTIONf_angle_d1.513983
X-RAY DIFFRACTIONf_dihedral_angle_d16.3393677
X-RAY DIFFRACTIONf_chiral_restr0.0581489
X-RAY DIFFRACTIONf_plane_restr0.0081882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.03460.29622320.26344397X-RAY DIFFRACTION95
2.0346-2.07160.29342340.25624456X-RAY DIFFRACTION95
2.0716-2.11150.28042320.25324404X-RAY DIFFRACTION95
2.1115-2.15460.28552330.24874430X-RAY DIFFRACTION95
2.1546-2.20140.2752340.2444441X-RAY DIFFRACTION95
2.2014-2.25260.28912320.24414397X-RAY DIFFRACTION95
2.2526-2.30890.28342330.23564433X-RAY DIFFRACTION95
2.3089-2.37140.24852340.23284439X-RAY DIFFRACTION94
2.3714-2.44110.26912320.23524421X-RAY DIFFRACTION94
2.4411-2.51990.27312330.23454415X-RAY DIFFRACTION95
2.5199-2.610.26162330.23054443X-RAY DIFFRACTION95
2.61-2.71450.26862340.23094433X-RAY DIFFRACTION95
2.7145-2.8380.26312340.2254447X-RAY DIFFRACTION95
2.838-2.98760.26942320.21544403X-RAY DIFFRACTION94
2.9876-3.17480.25372310.21074404X-RAY DIFFRACTION94
3.1748-3.41980.26362360.20414482X-RAY DIFFRACTION95
3.4198-3.76380.23092330.19514428X-RAY DIFFRACTION95
3.7638-4.30820.21112330.16224422X-RAY DIFFRACTION94
4.3082-5.42660.20972350.16194466X-RAY DIFFRACTION94
5.4266-47.31220.232390.2094531X-RAY DIFFRACTION94
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)
10.0030.0005-0.0009-0.00140.00290.0003-0.0170.00130.00470.0187-0.00550.0237-0.0096-0.0021-00.0622-0.00540.00160.04640.01350.0703-10.5509-14.7581-9.1714
20.0006-0.0003-00.0003-0.00030.0001-0.00490.0112-0.0022-0.0009-0.00030.00240.0002-000.0081-0.0024-0.03480.0280.01610.0312-12.8926-9.0736-18.7311
30.00010.0008-0.0008-0.0005-0.0008-0.0005-0.0034-0.00250.00290.0024-0.00960.0013-0.0039-0.00320-0.0135-0.0551-0.06270.00460.1183-0.0374-2.5233-10.3558-19.0904
40.0001-0.0026-0.00080.00090.00190.00090.00270.0202-0.02340.0149-0.00550.00890.00250.000400.03140.0153-0.01510.0360.03250.03925.3326-33.0415-18.7784
5000.00040.0003-0.00080.0003-0.00510.0033-0.00640.0191-0.00270.00870.0007-0.0044-00.053-0.00930.00290.04590.01460.053-1.5635-29.8393-1.3937
60.001-0.0022-0.00180.0001-0.0012-0.0006-0.00850.0053-0.00180.0018-0.01390.01060.0002-0.0052-00.01030.0140.01460.06240.03270.0601-4.51-22.948-27.4052
70.00160.0005-0.0016-0.0002-0.0011-0.00030.0082-0.0028-0.0010.00110.002-0.00520.00020.0052-00.0368-0.0376-0.01090.04610.06460.05439.2272-14.2808-20.0437
80.00180.00090.0007-0-0.0005-0.00020.0094-0.00450.01980.00390.0038-0.00480.00070.002-00.0562-0.0448-0.04360.05980.09720.04759.6981-13.1469-12.7645
90.00010.00160.00140.0006-0.0001-0.00040.0041-0.00270.001-0.00430.0042-0.0006-0.0054-0.000600.049-0.0103-0.08140.03370.01550.07752.9556-2.9881-7.0369
100.00090.0009-0.0001-0.0019-0.00320.0005-0.02390.0066-0.0043-0.0075-0.0245-0.0117-0.0112-0.0052-00.04760.0081-0.01270.028-0.00310.027335.7527-14.70838.436
11-00.000100.00010.00010-0.0063-0.00140.00030.0007-0.0034-0.001-0.0022-0.0018-00.03490.0161-0.01260.0316-0.00170.053738.1567-8.853817.9611
120.0005-0.0005-0.0013-0.00010.0008-0.00010.00210.00380.00690.0035-0.0128-0.0045-0.00480.0018-00.04050.0429-0.02180.0392-0.09340.012927.6814-10.12618.2595
130.001-0.00160.0006-0.00010.0001-0.0010.00620.0005-0.00380.0026-0.00110.0047-0.00620.0035-00.0006-0.0166-0.03170.0268-0.04390.031320.0148-28.942125.9803
14-00.00040.00090.0006-0.0002-0.00040.00310.0058-0.0056-0.01050.0090.00580.0031-0.006300.01290.0118-0.03720.0159-0.01470.046620.2087-35.12719.8356
15-0.00080.00170.001500.00070.0008-0.0113-0.0013-0.0014-0.0125-0.00410.0074-0.00370.001200.0706-0.0123-0.03760.041-0.0070.033218.3777-34.91926.0741
16-0-0.00020.0006-0.00020.00020.0003-0.00060.0018-0.003-0.00480.0031-0.00590.0016-0.0012-00.042-0.0057-0.00430.0355-0.0010.03332.813-29.16822.1814
170.00040.0019-0.00140.0007-0.00030-0.0069-0.00330.0019-0.0029-0.0147-0.00860.00360.0045-00.0456-0.0352-0.00330.0527-0.02570.029829.6711-22.756226.6564
180.00060.0005-0.0015-0.00050.000300.00150.0044-0.00060.0029-0.00550.006-0.008-0.000800.01260.0336-0.01030.0434-0.05420.025115.8722-14.119319.1918
190.0012-0.00080.0007-0.00080.001-0.00030.01020.00420.012-0.00390.00980.01750.00450.00120-0.00710.0454-0.02680.0207-0.06530.019215.6031-12.939411.9974
20-0.0001-0.00090.0010.00020.0001-0.00010.00210.00350.0020.00240.0003-0.0001-0.00510.0017-00.06550.0203-0.03360.0431-0.0040.066422.2331-2.83826.1115
210.00060.00010.0008-0.00030.0009-0.0001-0.00580.00180.0015-0.00690.00040.00180.006-0.0019-0-0.0123-0.02290.0020.0112-0.01060.017114.8462-40.9859-47.5006
220.00250.00270.0008-0.00040.00190.0004-0.0362-0.01870.0056-0.0254-0.02430.01260.0192-0.0066-00.00880.00940.01060.01880.0433-0.035422.2645-37.779-42.819
23-0.00420.00440.0038-0.0019-0.0005-00.0118-0.01170.0292-0.00170.0109-0.01790.0236-0.0052-0-0.05080.0365-0.01520.03580.0661-0.046732.987-30.3501-30.8077
24-0.00060.0005-0.00180.0001-0.00220.0009-0.0043-0.00520.0065-0.02690.0038-0.007-0.00570.009300.05730.02110.01250.02830.02780.037536.69-17.0682-46.2475
250.00160.00180.0001-0.0008-0.0011-0.00020.0056-0.0128-0.0034-0.0155-0.01320.0032-0.0084-0.005900.02910.015-0.00010.07290.00660.054824.6942-24.9574-40.552
260.0009-0.00050.0008-0.0012-0.0007-0.00040.00650.0024-0.0078-0.01450.0047-0.0204-0.0048-0.000300.02340.07920.0020.05090.09180.019539.3198-38.6753-37.4738
27-0.0002-0.0003-0.000600-00.00240.0029-0.0027-0.00210.0003-0.00090.0035-0.003900.0355-0.00160.05210.00910.01320.049834.0009-48.9756-48.4276
28-0.0002-0.00060.0003-0.00020.00040.0003-0.00580.0080.0015-0.0050.0027-0.00010.00160.00140-0.0042-0.0146-0.02910.010.0381-0.0023-11.065414.6939-45.8236
290.00010.0002-0.00040.0001-00.0006-0.0120.0046-0.00570.0008-0.00690.0008-0.00650.003600.0316-0.05230.01120.03030.01470.024-1.438112.2259-45.8065
300.00380.0032-0.0007-0.00070.0017-0.0005-0.01150.00240.0126-0.0146-0.00830.00670.00690.000400.0284-0.0034-0.00050.0313-0.00470.0356-2.73916.949-44.5488
310.0002-0.000100.0001000.0007-0.0027-0.0063-0.00180.00050.00160.00320.0001-00.03590.02440.0080.032-0.01860.0366-7.10849.5536-35.5112
32-0.00390.0028-0-0.00170.001-0.00290.0229-0.0190.0370.0007-0.0024-0.00620.01360.00690-0.06910.03140.0468-0.03530.054-0.10157.570821.3485-30.9787
3300.0021-0.00260.0004-0.00150.0009-0.00750.00590.0025-0.01320.0110.0017-0.00930.0034-00.0573-0.0030.00440.03360.03440.074311.690235.5597-45.5659
340.00130.00430.00070.0001-0.0009-0.0004-0.0062-0.01150.0054-0.0098-0.00250.0063-0.0055-0.002100.040.0085-0.01030.04420.02860.0555-0.391127.6922-39.822
350.00030.00050.00010.00020.00050.00020.00370.0102-0.0075-0.0002-0.0092-0.0001-0.0010.004-00.04390.00940.01010.05190.01950.033711.428613.3589-32.2981
360.0003-0.00050.0008-0.0005-0.0001-0.00040.006-0.0049-0.00240.00050.0044-0.0027-0.00520.0025-0-0.03270.04850.0206-0.03720.06630.044817.353311.9072-33.663
37-0.0007-0.0007-0.00190.00050.0010.00080.00150.0107-0.01230.0010.00360.00270.0040.0004-00.0462-0.0220.09360.01440.03020.022210.91169.7635-47.8638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 3 through 77 )
2X-RAY DIFFRACTION2chain 'C' and (resid 78 through 96 )
3X-RAY DIFFRACTION3chain 'C' and (resid 97 through 126 )
4X-RAY DIFFRACTION4chain 'C' and (resid 127 through 203 )
5X-RAY DIFFRACTION5chain 'C' and (resid 204 through 231 )
6X-RAY DIFFRACTION6chain 'C' and (resid 232 through 251 )
7X-RAY DIFFRACTION7chain 'C' and (resid 252 through 278 )
8X-RAY DIFFRACTION8chain 'C' and (resid 279 through 303 )
9X-RAY DIFFRACTION9chain 'C' and (resid 304 through 321 )
10X-RAY DIFFRACTION10chain 'A' and (resid 3 through 77 )
11X-RAY DIFFRACTION11chain 'A' and (resid 78 through 96 )
12X-RAY DIFFRACTION12chain 'A' and (resid 97 through 126 )
13X-RAY DIFFRACTION13chain 'A' and (resid 127 through 161 )
14X-RAY DIFFRACTION14chain 'A' and (resid 162 through 193 )
15X-RAY DIFFRACTION15chain 'A' and (resid 194 through 215 )
16X-RAY DIFFRACTION16chain 'A' and (resid 216 through 231 )
17X-RAY DIFFRACTION17chain 'A' and (resid 232 through 251 )
18X-RAY DIFFRACTION18chain 'A' and (resid 252 through 278 )
19X-RAY DIFFRACTION19chain 'A' and (resid 279 through 303 )
20X-RAY DIFFRACTION20chain 'A' and (resid 304 through 321 )
21X-RAY DIFFRACTION21chain 'B' and (resid 3 through 27 )
22X-RAY DIFFRACTION22chain 'B' and (resid 28 through 103 )
23X-RAY DIFFRACTION23chain 'B' and (resid 104 through 161 )
24X-RAY DIFFRACTION24chain 'B' and (resid 162 through 215 )
25X-RAY DIFFRACTION25chain 'B' and (resid 216 through 247 )
26X-RAY DIFFRACTION26chain 'B' and (resid 248 through 303 )
27X-RAY DIFFRACTION27chain 'B' and (resid 304 through 321 )
28X-RAY DIFFRACTION28chain 'D' and (resid 3 through 21 )
29X-RAY DIFFRACTION29chain 'D' and (resid 22 through 38 )
30X-RAY DIFFRACTION30chain 'D' and (resid 39 through 77 )
31X-RAY DIFFRACTION31chain 'D' and (resid 78 through 96 )
32X-RAY DIFFRACTION32chain 'D' and (resid 97 through 161 )
33X-RAY DIFFRACTION33chain 'D' and (resid 162 through 215 )
34X-RAY DIFFRACTION34chain 'D' and (resid 216 through 247 )
35X-RAY DIFFRACTION35chain 'D' and (resid 248 through 272 )
36X-RAY DIFFRACTION36chain 'D' and (resid 273 through 292 )
37X-RAY DIFFRACTION37chain 'D' and (resid 293 through 321 )

+
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