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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wbq
TitleCrystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L] mutant E212Q complexed with L-TA.
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / cis-Epoxysuccinate Hydrolases / epoxide hydrolase / L(+)-tartaric acid
Function / homologyhydrolase activity, acting on acid halide bonds, in C-halide compounds / L-2-Haloacid dehalogenase / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / L(+)-TARTARIC ACID / Epoxide hydrolase
Function and homology information
Biological speciesRhodococcus opacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

-
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)59,0024
Polymers58,7022
Non-polymers3002
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.643, 53.888, 61.959
Angle α, β, γ (deg.)67.070, 75.840, 75.970
Int Tables number1
Space group name H-MP1
Space group name HallP1

-
Components

#1: Protein Epoxide hydrolase /


Mass: 29350.924 Da / Num. of mol.: 2 / Mutation: E212Q
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-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium citrate tribasic, 0.2M potassium acetate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.978557 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978557 Å / Relative weight: 1
ReflectionResolution: 2.2→56.25 Å / Num. obs: 23063 / % possible obs: 98.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.52 Å2 / CC1/2: 0.926 / Rmerge(I) obs: 0.245 / Rpim(I) all: 0.16 / Rrim(I) all: 0.294 / Χ2: 0.66 / Net I/σ(I): 5.8
Reflection shellResolution: 2.2→2.26 Å / % possible obs: 97.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 1.221 / Num. measured all: 4933 / Num. unique obs: 1694 / CC1/2: 0.264 / Rpim(I) all: 0.875 / Rrim(I) all: 1.514 / Χ2: 0.56 / Net I/σ(I) obs: 3.3

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→56.25 Å / SU ML: 0.2493 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2395 1212 5.27 %
Rwork0.1825 21768 -
obs0.1855 22980 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.73 Å2
Refinement stepCycle: LAST / Resolution: 2.2→56.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 18 116 3929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413891
X-RAY DIFFRACTIONf_angle_d0.65675281
X-RAY DIFFRACTIONf_chiral_restr0.04587
X-RAY DIFFRACTIONf_plane_restr0.0055687
X-RAY DIFFRACTIONf_dihedral_angle_d12.2101541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.290.31611370.23342338X-RAY DIFFRACTION95.86
2.29-2.390.27971340.21062431X-RAY DIFFRACTION96.98
2.39-2.520.29651280.21332392X-RAY DIFFRACTION97.22
2.52-2.680.25991430.19732433X-RAY DIFFRACTION97.8
2.68-2.880.29751330.19692409X-RAY DIFFRACTION98.03
2.88-3.170.2451450.19152428X-RAY DIFFRACTION98.39
3.17-3.630.23321320.17072444X-RAY DIFFRACTION98.66
3.63-4.580.21361230.15422464X-RAY DIFFRACTION99
4.58-56.250.18211370.16962429X-RAY DIFFRACTION98.28
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)
16.986772131743.28208948056-4.937288345184.32439028536-3.521537694327.18029889580.161417777329-0.1391362131990.1590676726250.511210548164-0.008942513179630.137783784866-0.467725913435-0.112967786022-0.1223860281090.213919678020.0160850978588-0.00814710705670.2040191475380.04197764263860.11498547550313.385311246616.416812415929.5203497556
26.648016186190.130898783194-2.893367742621.673944553420.3637544006452.8048362644-0.125668885191-0.4201446760690.22860523780.216978957197-0.401822569711-0.229090547389-0.2295043629910.4421969519990.3166168145670.2766770192470.0163496120553-0.0002404208634420.4895745629230.1125848563270.1576098851418.52198950298.037293939536.4544489851
32.865890143181.06337777195-2.690862746322.43250214149-0.2126945585532.86121642824-0.210516619377-0.0525710650569-0.466112441429-0.320868413573-0.152448508959-0.101724790350.3946622940240.2148917193740.3003048405160.2182694284850.03558800108810.04784525572820.3003020967840.1442703489390.22344425990818.82180828850.81879103170630.197899876
42.106239104461.97770318342-0.8530666783734.31169139456-0.9006407069941.47061506389-0.182826753755-0.009372507033970.00700010494741-0.1344111169050.1747036024350.0607338282635-0.0233548386236-0.341783081108-0.06650231117470.2019286743450.0411967165607-0.007150346094180.2971850891920.06313576254360.12396582087110.25431998913.388890498128.0222527988
52.301925723410.500497899043-0.8971750918663.31088258627-0.7794829533532.08383596029-0.09752273324730.0092195684805-0.2125216544250.0296405673671-0.091726726541-0.248555587888-0.2147077066970.3110328597360.1790859443030.20811765821-0.03291500712140.002293582533380.3109245940090.09175810861320.14739241941422.704070281414.861444717717.3222402917
67.35531613748-1.50017888351-2.696084584825.46921645152.961291016226.06005931384-0.214167278186-0.1915725339320.2054381928250.264084961198-0.18541693597-0.6106516081330.1983292967610.8254106500280.3947746530290.249433652406-0.11048593357-0.05332409886130.5564849713580.1069936252510.33519290857632.15895019120.895204663522.2593159031
73.61536020988-0.0678816983684-2.438382258171.066315762960.8317758135462.716772474930.110238260444-0.9271487170370.1566387840180.637746362889-0.303260597067-0.423770621753-0.4624065378290.7049991450290.138014757260.584959683424-0.189286917992-0.07732050164690.436586135013-0.01412968161570.22693248653524.753130641528.154794664729.8153279736
81.34353502267-0.3175548809440.2652617031990.3818349230170.1822789629390.393442842311-0.0380953170980.2129078528370.03680443390090.1263755456190.1735386467820.148183994844-0.125891584701-0.262102122276-0.1077867912930.2187580317030.02802275640190.01431879798770.4147337099280.1447125108230.23957479803212.561686228417.5978141159-4.01418874933
91.803188524640.665324752163-1.076706547494.12592496854-0.6758495418122.77891454527-0.04242376565040.301816979893-0.239985408635-0.219409356989-0.1913630947230.2033171487610.2512849365920.2929182439070.1444139054120.2351624713820.01752667249750.0689787334050.4786885324350.2030982604230.17380441615829.489903718416.5407217006-11.9291956521
102.11684756697-0.07866052219940.06983643395052.05835246435-0.4915771557363.04620625649-0.004698777254710.199530868161-0.0344865967331-0.120822863365-0.0225699727289-0.05443461018560.165093247599-0.08536865480350.0359174217720.194762740949-0.009230873322690.03205966818570.2647212467410.09049484090490.12468254113513.896917456911.37882727822.61424753654
111.869310636392.20527872246-2.127311322113.75853609304-3.502459261844.14060376396-0.1973781903450.5539565247070.118833648955-0.8441518390580.1543703028910.365647224830.298474924534-0.747712358765-0.05559290131520.333792775379-0.0505662466964-0.06375608351760.5596965833060.1284447983320.2237846930333.5619214075614.0605531011-7.39473139088
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 43 )AA11 - 431 - 33
22chain 'A' and (resid 44 through 67 )AA44 - 6734 - 57
33chain 'A' and (resid 68 through 88 )AA68 - 8858 - 78
44chain 'A' and (resid 89 through 125 )AA89 - 12579 - 115
55chain 'A' and (resid 126 through 177 )AA126 - 177116 - 167
66chain 'A' and (resid 178 through 200 )AA178 - 200168 - 190
77chain 'A' and (resid 201 through 246 )AA201 - 246191 - 236
88chain 'B' and (resid 3 through 43 )BC3 - 431 - 41
99chain 'B' and (resid 44 through 108 )BC44 - 10842 - 106
1010chain 'B' and (resid 109 through 207 )BC109 - 207107 - 205
1111chain 'B' and (resid 208 through 246 )BC208 - 246206 - 244

+
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