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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.287 (Depositor), 0.241 (DCC)
R-Value Work:
0.194 (Depositor), 0.172 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 1QH9

This is version 2.0 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q53464
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LAC Query on LAC Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	LACTIC ACID C₃ H₆ O₃ JVTAAEKCZFNVCJ-UWTATZPHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.287 (Depositor), 0.241 (DCC)
R-Value Work: 0.194 (Depositor), 0.172 (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

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Entry History

Deposition Data

Released Date: 2000-05-24

Deposition Author(s):

Revision History (Full details and data files)

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

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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.