5GZY

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 ?
R-Value Free: 0.197
R-Value Work: 0.158
R-Value Observed: 0.160

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

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

Wang, Y., Xue, S.

To be published.

Macromolecule Content

Total Structure Weight: 136.42 kDa
Atom Count: 10,832
Modelled Residue Count: 1,168
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2OP Query on 2OP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	(2S)-2-HYDROXYPROPANOIC ACID C₃ H₆ O₃ JVTAAEKCZFNVCJ-REOHCLBHSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 ?
R-Value Free: 0.197
R-Value Work: 0.158
R-Value Observed: 0.160
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	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

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Entry History

Deposition Data

Released Date: 2017-10-04

Deposition Author(s):

Wang, Y.

Xue, 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
Version 1.2: 2023-11-15
Changes: Data collection

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Help and Resources

5GZY

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)