8HP6 | pdb_00008hp6

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: in silico

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	D [auth A], E [auth B], F [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

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

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-21 
Deposition Author(s): Yang, Q., Wang, L., Xu, X., Xing, X., Zhou, J.

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

Revision History  

• Version 1.0: 2023-06-21
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection