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- PDB-5xmd: Crystal structure of epoxide hydrolase VrEH1 from Vigna radiata -

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Basic information

Entry
Database: PDB / ID: 5xmd
TitleCrystal structure of epoxide hydrolase VrEH1 from Vigna radiata
ComponentsEpoxide hydrolase A
KeywordsHYDROLASE / Epoxide hydrolase Enantioconvergent
Function / homology
Function and homology information


epoxide 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
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKong, X.D. / Xu, J.H. / Zhou, J.H.
CitationJournal: to be published
Title: Crystal structure of Carboxyl reductase
Authors: Kong, X.D. / Xu, J.H. / Zhou, J.H.
History
DepositionMay 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)157,3674
Polymers157,3674
Non-polymers00
Water9,782543
1
A: Epoxide hydrolase A

C: Epoxide hydrolase A


Theoretical massNumber of molelcules
Total (without water)78,6832
Polymers78,6832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
2
B: Epoxide hydrolase A

D: Epoxide hydrolase A


Theoretical massNumber of molelcules
Total (without water)78,6832
Polymers78,6832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-x-1,y-1/2,-z-11
Unit cell
Length a, b, c (Å)101.691, 51.892, 124.294
Angle α, β, γ (deg.)90.000, 94.270, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

#1: Protein
Epoxide hydrolase A


Mass: 39341.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna radiata (mung bean) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E5L4L1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 285 SHOULD BE PRO AND WAS CONFIRMED BY SEQUENCING OF THE ORIGINAL CONSTRUCT. THE CONFLICT ...RESIDUE 285 SHOULD BE PRO AND WAS CONFIRMED BY SEQUENCING OF THE ORIGINAL CONSTRUCT. THE CONFLICT SHOULD BE DUE TO MISTAKE IN SEQUENCE REFERENCE E5L4L1_VIGRA.

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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: 2.27 Å3/Da / Density % sol: 40.81 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1M Hepes pH 6.5-7.0, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 82570 / % possible obs: 93.7 % / Redundancy: 4.5 % / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.721

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PHASERphasing
PDB_EXTRACT3.14data extraction
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJP

2cjp


Resolution: 2→41.316 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.67
RfactorNum. reflection% reflection
Rfree0.2226 4127 5 %
Rwork0.1795 --
obs0.1817 82530 93.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.06 Å2 / Biso mean: 33.2579 Å2 / Biso min: 14.25 Å2
Refinement stepCycle: final / Resolution: 2→41.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9969 0 0 543 10512
Biso mean--0 35.84 -
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810281
X-RAY DIFFRACTIONf_angle_d1.04713986
X-RAY DIFFRACTIONf_chiral_restr0.0741502
X-RAY DIFFRACTIONf_plane_restr0.0051795
X-RAY DIFFRACTIONf_dihedral_angle_d14.1423741
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9978-2.02130.31021370.26422495263289
2.0213-2.04590.29671640.25042713287795
2.0459-2.07180.31451430.23462785292895
2.0718-2.09910.27511490.22462656280595
2.0991-2.12780.32921550.22652695285095
2.1278-2.15820.26681380.21152765290394
2.1582-2.19040.27711380.20872664280294
2.1904-2.22470.24931250.22312686281194
2.2247-2.26110.28261390.22042710284993
2.2611-2.30010.30321260.20882662278894
2.3001-2.34190.23111210.20132690281192
2.3419-2.3870.27841410.19482624276592
2.387-2.43570.26331190.19762664278392
2.4357-2.48860.2521360.20122645278191
2.4886-2.54650.24071520.19732601275392
2.5465-2.61020.2981460.18842592273890
2.6102-2.68080.27211470.19772615276291
2.6808-2.75960.23971500.19832581273190
2.7596-2.84870.26521170.20622690280792
2.8487-2.95050.26571480.2142624277292
2.9505-3.06860.23941630.21162688285193
3.0686-3.20820.25441480.1992768291695
3.2082-3.37720.22791410.18812796293796
3.3772-3.58870.2411340.17752669280392
3.5887-3.86560.19591440.15132676282091
3.8656-4.25430.16151590.14462830298997
4.2543-4.86910.14971480.12952895304399
4.8691-6.13130.17021410.15382948308999
6.1313-41.32510.16581580.1492976313497

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