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

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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 A0ABX8E6T6 (Novosphingobium decolorationis) Explore A0ABX8E6T6 Go to UniProtKB: A0ABX8E6T6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABX8E6T6
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 F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	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 H [auth C] SDF format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] mmCIF format, chain H [auth C] mmCIF format, chain G [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