8HP7 | pdb_00008hp7

Crystal structure of (S)-2-haloacid dehalogenase K152A mutant trapped with (2R)-4-amino-2-hydroxybutanoic acid

PDB DOI: https://doi.org/10.2210/pdb8HP7/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: 1.43 Å
R-Value Free:
0.211 (Depositor), 0.211 (DCC)
R-Value Work:
0.193 (Depositor), 0.193 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 2.1 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: 99.14 kDa
Atom Count: 6,860
Modeled Residue Count: 723
Deposited Residue Count: 867
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 A0ACD6B9T8 (Novosphingobium sp. MBES04) Explore A0ACD6B9T8 Go to UniProtKB: A0ACD6B9T8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9T8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ABU (Subject of Investigation/LOI) Query on ABU 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] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-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]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain H [auth C] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C]	G [auth C], H [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain G [auth C] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.211 (Depositor), 0.211 (DCC)
R-Value Work: 0.193 (Depositor), 0.193 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.987	α = 90
b = 84.221	β = 133.93
c = 102.356	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection
Version 2.1: 2024-11-13
Changes: Structure summary

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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.