5H00 | pdb_00005h00

The crystal structure of D-2-haloacid dehalogenase

PDB DOI: https://doi.org/10.2210/pdb5H00/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free:
0.251 (Depositor), 0.250 (DCC)
R-Value Work:
0.193 (Depositor), 0.200 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of D-2-haloacid dehalogenase

Wang, Y., Xue, S.

To be published.

Macromolecule Content

Total Structure Weight: 136.06 kDa
Atom Count: 9,561
Modeled Residue Count: 1,158
Deposited Residue Count: 1,204
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q52086
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.251 (Depositor), 0.250 (DCC)
R-Value Work: 0.193 (Depositor), 0.200 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.715	α = 90
b = 109.396	β = 90
c = 138.656	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-10-04

Deposition Author(s):

Revision History (Full details and data files)

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

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.