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- PDB-5y5d: The crystal structure of VrEH2 mutant M263W -

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Basic information

Entry
Database: PDB / ID: 5y5d
TitleThe crystal structure of VrEH2 mutant M263W
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / Epoxide hydrolase
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
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsXu, J.H. / Yu, H.L. / Zhou, J.H. / Kong, X.D. / Li, F.L.
CitationJournal: To Be Published
Title: The crystal structure of VrEH2 mutant M263W
Authors: Xu, J.H. / Yu, H.L. / Zhou, J.H. / Kong, X.D. / Li, F.L.
History
DepositionAug 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Revision 1.2Nov 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
B: Epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)37,3881
Polymers37,3881
Non-polymers00
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12570 Å2
Unit cell
Length a, b, c (Å)70.475, 70.475, 129.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-629-

HOH

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Components

#1: Protein Epoxide hydrolase /


Mass: 37388.359 Da / Num. of mol.: 1 / Mutation: G3F, V4I, M263W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna radiata (mung bean) / Gene: EH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0R5NGA4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.59 % / Description: rhombus
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG3350, Tris-HCL, Ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 28594 / % possible obs: 99.7 % / Observed criterion σ(I): 0.9 / Redundancy: 24.5 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 38.444
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 21.4 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 28594 / Rsym value: 0.866 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XM6

5xm6


Resolution: 1.85→25.422 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.29
RfactorNum. reflection% reflection
Rfree0.2359 1358 5.04 %
Rwork0.2051 --
obs0.2067 26965 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→25.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 0 322 2887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082643
X-RAY DIFFRACTIONf_angle_d1.0953598
X-RAY DIFFRACTIONf_dihedral_angle_d15.149955
X-RAY DIFFRACTIONf_chiral_restr0.077377
X-RAY DIFFRACTIONf_plane_restr0.006465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8481-1.91410.30821020.26831947X-RAY DIFFRACTION73
1.9141-1.99070.36721150.26022148X-RAY DIFFRACTION81
1.9907-2.08130.31881360.24662390X-RAY DIFFRACTION90
2.0813-2.1910.28541040.23812653X-RAY DIFFRACTION98
2.191-2.32820.2841390.22522680X-RAY DIFFRACTION100
2.3282-2.50780.24431580.22182679X-RAY DIFFRACTION100
2.5078-2.75990.22471520.21682692X-RAY DIFFRACTION100
2.7599-3.15860.24451560.20942710X-RAY DIFFRACTION100
3.1586-3.9770.20311480.17612784X-RAY DIFFRACTION100
3.977-25.42410.1821480.17162924X-RAY DIFFRACTION100

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