5YB5 | pdb_00005yb5

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 (Depositor), 0.251 (DCC)
R-Value Work:
0.193 (Depositor), 0.199 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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
Modeled Residue Count: 318
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epoxide hydrolase	A [auth B]	326	Vigna radiata	Mutation(s): 3 Gene Names: EH2 EC: 3.3.2.10
UniProt
Find proteins for A0A0R5NGA4 (Vigna radiata) Explore A0A0R5NGA4 Go to UniProtKB: A0A0R5NGA4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.251 (DCC)
R-Value Work: 0.193 (Depositor), 0.199 (DCC)
R-Value Observed: 0.196 (Depositor)

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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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.