[English] 日本語
Yorodumi
- PDB-8wbn: Crystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L] muta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wbn
TitleCrystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L] mutant D193N
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / cis-Epoxysuccinate Hydrolases / epoxide hydrolase / L(+)-tartaric acid
Function / homologyhydrolase activity, acting on halide bonds, in C-halide compounds / L-2-Haloacid dehalogenase / : / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Epoxide hydrolase
Function and homology information
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDong, S. / Xuan, J.S. / Feng, Y.G. / Cui, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171203 China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Deciphering the stereo-specific catalytic mechanisms of cis-epoxysuccinate hydrolases producing L(+)-tartaric acid.
Authors: Dong, S. / Xuan, J. / Feng, Y. / Cui, Q.
History
DepositionSep 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epoxide hydrolase
B: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8944
Polymers58,7022
Non-polymers1922
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-45 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.404, 58.552, 64.086
Angle α, β, γ (deg.)69.88, 73.55, 82.69
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Epoxide hydrolase


Mass: 29350.920 Da / Num. of mol.: 2 / Mutation: D193N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus opacus (bacteria) / Gene: eph / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1KLR5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium sulfate, 0.1M Bis-tris, pH6.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→48.55 Å / Num. obs: 17521 / % possible obs: 89.1 % / Redundancy: 1.9 % / CC1/2: 0.979 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.091 / Rrim(I) all: 0.129 / Χ2: 0.66 / Net I/σ(I): 4.3 / Num. measured all: 33094
Reflection shellResolution: 2.5→2.6 Å / % possible obs: 89.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.312 / Num. measured all: 3751 / Num. unique obs: 1990 / CC1/2: 0.824 / Rpim(I) all: 0.31 / Rrim(I) all: 0.44 / Χ2: 0.56 / Net I/σ(I) obs: 1.6

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→38.9 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 859 4.91 %
Rwork0.2106 --
obs0.2133 17508 89.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 10 13 3739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023812
X-RAY DIFFRACTIONf_angle_d0.575185
X-RAY DIFFRACTIONf_dihedral_angle_d12.511373
X-RAY DIFFRACTIONf_chiral_restr0.039578
X-RAY DIFFRACTIONf_plane_restr0.005671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.32671370.25842858X-RAY DIFFRACTION91
2.66-2.860.33091580.24542821X-RAY DIFFRACTION92
2.86-3.150.29321490.24272773X-RAY DIFFRACTION89
3.15-3.610.33031320.23632591X-RAY DIFFRACTION83
3.61-4.540.22161530.18412804X-RAY DIFFRACTION90
4.54-38.90.22681300.19062802X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.05940.4817-0.63160.7180.7411.1017-0.40830.77490.0997-0.65870.1534-0.13860.1121-0.41440.12710.4892-0.0901-0.00550.54520.00910.3756-3.951922.50625.7854
21.1176-0.533-0.01144.9218-2.39644.5209-0.20320.44450.0008-0.238-0.0237-0.16030.1032-0.14740.22410.4613-0.122-0.00650.7842-0.14020.47475.682815.110620.6577
38.21062.7225-2.87571.0526-0.85251.44950.12050.30720.5563-0.04810.11250.1198-0.29970.1628-0.25450.6378-0.18160.02450.702-0.07030.4317-1.112724.184627.9136
43.59341.19791.31760.35420.55382.44840.07440.2865-0.3455-0.20980.0628-0.01310.22480.0891-0.15240.5023-0.09490.0390.5387-0.06990.4076-7.17839.461233.9877
50.90631.37110.4975.44661.24043.2727-0.26190.560.0864-0.68570.17080.0465-0.3390.16560.10960.4549-0.1495-0.09040.7010.00880.3522-21.428711.851930.0043
62.65021.5638-0.29753.5566-2.17543.11620.4758-0.73360.14680.4989-0.21130.0791-0.31780.4702-0.26230.4324-0.10260.02720.634-0.12820.3488-6.822813.873164.4597
79.2759-0.3606-2.92163.1076-0.5734.24780.75-0.9212-0.04680.3446-0.8027-0.3131-0.71380.22280.12310.6218-0.2524-0.1610.73840.110.5187-0.22095.455370.354
84.54050.9909-2.23012.956-2.35544.1944-0.07310.0101-0.6343-0.0098-0.1983-0.38440.37120.15830.08880.5131-0.11740.00580.57010.00240.4613-5.5171-1.131365.5806
93.72270.25130.14316.4901-1.83764.80740.2-0.18120.4140.1146-0.34770.9221-0.0699-0.61170.2570.36690.0256-0.01150.5779-0.0560.4237-7.151624.359857.0067
102.64560.81260.45441.3758-0.36252.83790.4742-0.4814-0.12080.0556-0.35180.04610.00380.0476-0.11940.3826-0.1057-0.02810.58210.00580.343-2.330615.206751.053
112.9343.6154-2.88569.8803-5.41367.25080.42510.1254-0.59270.2475-0.667-0.88770.09321.20380.04850.4421-0.0898-0.01740.6693-0.06150.446911.247811.815950.8471
123.99472.3375-3.34363.7306-1.52756.24670.0369-0.4079-0.610.3977-0.5521-0.6207-0.13980.15880.32640.4398-0.1482-0.05110.8023-0.02690.46928.347520.820860.9269
133.84641.8022-1.64486.3494-3.55996.48590.3001-0.4246-0.20330.8235-0.0738-0.0862-0.83760.9637-0.18110.5963-0.21990.03870.7192-0.15930.57494.511730.46962.087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 217 )
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 247 )
6X-RAY DIFFRACTION6chain 'B' and (resid 11 through 43 )
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 67 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 108 )
9X-RAY DIFFRACTION9chain 'B' and (resid 109 through 125 )
10X-RAY DIFFRACTION10chain 'B' and (resid 126 through 160 )
11X-RAY DIFFRACTION11chain 'B' and (resid 161 through 177 )
12X-RAY DIFFRACTION12chain 'B' and (resid 178 through 217 )
13X-RAY DIFFRACTION13chain 'B' and (resid 218 through 247 )

+
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