5GKW

crystal structure of SZ529 complex with (R,R)-cyclopentanediol

PDB DOI: https://doi.org/10.2210/pdb5GKW/pdb

Classification: HYDROLASE
Organism(s): Rhodococcus erythropolis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-07-07 Released: 2017-07-12
Deposition Author(s): Wu, L., Sun, Z.T., Reetz, M.T., Zhou, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.263
R-Value Work: 0.226
R-Value Observed: 0.228

wwPDB Validation 3D Report Full Report

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

Literature

crystal structure of SZ529 complex with (R,R)-cyclopentanediol

Wu, L., Sun, Z.T., Reetz, M.T., Zhou, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 34.74 kDa
Atom Count: 2,166
Modelled Residue Count: 260
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Limonene-1,2-epoxide hydrolase	A, B	155	Rhodococcus erythropolis	Mutation(s): 4 Gene Names: limA EC: 3.3.2.8
UniProt
Find proteins for Q9ZAG3 (Rhodococcus erythropolis) Explore Q9ZAG3 Go to UniProtKB: Q9ZAG3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ZAG3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6VV Query on 6VV Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(1~{R},2~{R})-cyclopentane-1,2-diol C₅ H₁₀ O₂ VCVOSERVUCJNPR-RFZPGFLSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.263
R-Value Work: 0.226
R-Value Observed: 0.228
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.856	α = 90
b = 60.541	β = 90
c = 119.272	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PHENIX	phasing
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-07-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-12
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 R01GM133198.