5GZY | pdb_00005gzy

The complex structure of D-2-haloacid dehalogenase with L-LA

• PDB DOI: https://doi.org/10.2210/pdb5GZY/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-02 Released: 2017-10-04 
• Deposition Author(s): Wang, Y., Xue, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.197 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

The complex structure of D-2-haloacid dehalogenase with L-LA

Wang, Y., Xue, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 136.42 kDa 
• Atom Count: 10,832 
• Modeled Residue Count: 1,168 
• Deposited Residue Count: 1,204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(R)-2-haloacid dehalogenase	A, B, C, D	301	Pseudomonas putida	Mutation(s): 0  Gene Names: hadD EC: 3.8.1.9
UniProt
Find proteins for Q52086 (Pseudomonas putida) Explore Q52086  Go to UniProtKB:  Q52086

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2OP	E [auth A], F [auth B], G [auth C], H [auth D]	(2S)-2-HYDROXYPROPANOIC ACID C3 H6 O3 JVTAAEKCZFNVCJ-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.197 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.945	α = 90
b = 95.136	β = 98.09
c = 109.058	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	data processing
Coot	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-04 
Deposition Author(s): Wang, Y., Xue, S.

Revision History  

• Version 1.0: 2017-10-04
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection