5GKW | pdb_00005gkw

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 (Depositor), 0.269 (DCC)
R-Value Work:
0.226 (Depositor), 0.237 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 260
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.269 (DCC)
R-Value Work: 0.226 (Depositor), 0.237 (DCC)
R-Value Observed: 0.228 (Depositor)

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

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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

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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.