1QH9 | pdb_00001qh9

ENZYME-PRODUCT COMPLEX OF L-2-HALOACID DEHALOGENASE

• PDB DOI: https://doi.org/10.2210/pdb1QH9/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas sp. YL
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-05-12 Released: 2000-05-24 
• Deposition Author(s): Li, Y.-F., Hata, Y., Fujii, T., Kurihara, T., Esaki, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.287 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.170 (DCC) 

Literature

The Structure of L-2-Haloacid Dehalogenase Complexed with a Reaction Product Reveals the Mechanism of Intermediate Hydrolysis in Dehalogenase

Li, Y.-F., Hata, Y., Fujii, T., Kurihara, T., Esaki, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 26.3 kDa 
• Atom Count: 1,763 
• Modeled Residue Count: 221 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-HALOACID DEHALOGENASE	A	232	Pseudomonas sp. YL	Mutation(s): 0  Gene Names: DEX YL EC: 3.8.1.2
UniProt
Find proteins for Q53464 (Pseudomonas sp. (strain YL)) Explore Q53464  Go to UniProtKB:  Q53464

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LAC	B [auth A]	LACTIC ACID C3 H6 O3 JVTAAEKCZFNVCJ-UWTATZPHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.287 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.170 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.81	α = 90
b = 62.76	β = 123.07
c = 51.38	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
PROCESS	data reduction
PROCESS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-05-24 
Deposition Author(s): Li, Y.-F., Hata, Y., Fujii, T., Kurihara, T., Esaki, N.

Revision History  

• Version 1.0: 2000-05-24
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations