8HP6

Crystal structure of (S)-2-haloacid dehalogenase D12A mutant

PDB DOI: https://doi.org/10.2210/pdb8HP6/pdb

Classification: HYDROLASE
Organism(s): Novosphingobium sp. MBES04
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-12-12 Released: 2023-06-21
Deposition Author(s): Yang, Q., Wang, L., Xu, X., Xing, X., Zhou, J.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.201
R-Value Work: 0.166
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Enzymatic hydrolysis on L-azetidine-2-carboxylate ring opening

Xu, X., Yang, Q., Wang, L., Zheng, J., Gu, Y., Xing, X.W., Zhou, J.

(2023) Catal Sci Technol

DOI: https://doi.org/10.1039/D3CY00366C

Macromolecule Content

Total Structure Weight: 98.82 kDa
Atom Count: 6,534
Modelled Residue Count: 720
Deposited Residue Count: 867
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(S)-2-haloacid dehalogenase	A, B, C	289	Novosphingobium sp. MBES04	Mutation(s): 1 Gene Names: MBENS4_0996
UniProt
Find proteins for A0A0S6WSA3 (Novosphingobium sp. MBES04) Explore A0A0S6WSA3 Go to UniProtKB: A0A0S6WSA3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0S6WSA3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.201
R-Value Work: 0.166
R-Value Observed: 0.168
Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.726	α = 90
b = 151.726	β = 90
c = 151.726	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2018YFA0901900

Revision History (Full details and data files)

Version 1.0: 2023-06-21
Type: Initial release

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 R01GM133198.