[English] 日本語
Yorodumi
- PDB-5xm6: the overall structure of VrEH2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xm6
Titlethe overall structure of VrEH2
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / epoxide hydrolase
Function / homology
Function and homology information


Hydrolases; Acting on ether bonds; Ether hydrolases / soluble epoxide hydrolase / epoxide hydrolase activity / hydrolase activity
Similarity search - Function
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
Epoxide hydrolase / soluble epoxide hydrolase
Similarity search - Component
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsLi, F.L. / Kong, X.D. / Yu, H.L. / Shang, Y.P. / Zhou, J.H. / Xu, J.H.
CitationJournal: Acs Catalysis / Year: 2018
Title: Regioselectivity Engineering of Epoxide Hydrolase: Near-Perfect Enantioconvergence through a Single Site Mutation
Authors: Li, F.L. / Kong, X.D. / Chen, Q. / Zheng, Y.C. / Xu, Q. / Chen, F.F. / Fan, L.Q. / Lin, G.Q. / Zhou, J.H. / Yu, H.L. / Xu, J.H.
History
DepositionMay 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epoxide hydrolase
B: Epoxide hydrolase
C: Epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)119,4453
Polymers119,4453
Non-polymers00
Water10,305572
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-2 kcal/mol
Surface area35970 Å2
Unit cell
Length a, b, c (Å)109.180, 109.180, 236.967
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Epoxide hydrolase


Mass: 39815.141 Da / Num. of mol.: 3 / Mutation: G3E, V4I, R114H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna radiata (mung bean) / Gene: Vreh3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0G3F3K2, UniProt: A0A0R5NGA4*PLUS, Hydrolases; Acting on ether bonds; Ether hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 3.25 Å3/Da / Density % sol: 62.1 % / Description: rhombus
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 20000, PEG500MME, HEPES, Mops, sodium nitrate, ammonium sulfate, disodium hydrogen phosphate.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 50435 / % possible obs: 100 % / Redundancy: 27.9 % / CC1/2: 0.987 / Rpim(I) all: 0.031 / Χ2: 1.022 / Net I/σ(I): 8.25
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 29.5 % / Num. unique obs: 4938 / CC1/2: 0.987 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4i6.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJP

2cjp


Resolution: 2.501→41.532 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.78
RfactorNum. reflection% reflection
Rfree0.2231 2556 5.08 %
Rwork0.18 --
obs0.1822 50310 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→41.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7678 0 0 572 8250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087906
X-RAY DIFFRACTIONf_angle_d1.11910757
X-RAY DIFFRACTIONf_dihedral_angle_d14.1362868
X-RAY DIFFRACTIONf_chiral_restr0.0771132
X-RAY DIFFRACTIONf_plane_restr0.0061392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.54910.28931340.20962586X-RAY DIFFRACTION99
2.5491-2.60110.28111500.20562614X-RAY DIFFRACTION100
2.6011-2.65770.29481280.21292611X-RAY DIFFRACTION100
2.6577-2.71950.26181370.19672620X-RAY DIFFRACTION100
2.7195-2.78750.2531350.19682600X-RAY DIFFRACTION100
2.7875-2.86280.24461510.19142610X-RAY DIFFRACTION100
2.8628-2.9470.26031430.19832624X-RAY DIFFRACTION100
2.947-3.04210.24131380.19642619X-RAY DIFFRACTION100
3.0421-3.15080.25291380.19122625X-RAY DIFFRACTION100
3.1508-3.27690.28621280.19762629X-RAY DIFFRACTION100
3.2769-3.4260.22481430.18182658X-RAY DIFFRACTION100
3.426-3.60650.19031420.17942628X-RAY DIFFRACTION100
3.6065-3.83230.21541410.17562659X-RAY DIFFRACTION100
3.8323-4.1280.19711560.16072649X-RAY DIFFRACTION100
4.128-4.54290.17851610.14942695X-RAY DIFFRACTION100
4.5429-5.19920.20261360.15222698X-RAY DIFFRACTION100
5.1992-6.54630.20881510.19092731X-RAY DIFFRACTION100
6.5463-41.53820.20781440.17952898X-RAY DIFFRACTION99

+
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