5YB5

The complex crystal structure of VrEH2 mutant M263N with SNO

PDB DOI: https://doi.org/10.2210/pdb5YB5/pdb

Classification: HYDROLASE
Organism(s): Vigna radiata
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-09-03 Released: 2018-09-05
Deposition Author(s): Li, F.L., Chen, F.F., Chen, Q., Kong, X.D., Yu, H.L., Xu, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.252
R-Value Work: 0.193
R-Value Observed: 0.196

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Regioselectivity Engineering of Epoxide Hydrolase: Near-Perfect Enantioconvergence through a Single Site Mutation

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.

(2018) ACS Catal 8: 8314-8317

DOI: https://doi.org/10.1021/acscatal.8b02622

Macromolecule Content

Total Structure Weight: 37.48 kDa
Atom Count: 2,720
Modelled Residue Count: 318
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epoxide hydrolase	A [auth B]	326	Vigna radiata	Mutation(s): 3 Gene Names: EH2
UniProt
Find proteins for A0A0R5NGA4 (Vigna radiata) Explore A0A0R5NGA4 Go to UniProtKB: A0A0R5NGA4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0R5NGA4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SNO Query on SNO Download Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	(S)-PARA-NITROSTYRENE OXIDE C₈ H₇ N O₃ YKIUTLHCSNCTDZ-MRVPVSSYSA-N		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.252
R-Value Work: 0.193
R-Value Observed: 0.196
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.297	α = 90
b = 70.297	β = 90
c = 121.295	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-09-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-09-05
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.