5JPU | pdb_00005jpu

Structure of limonene epoxide hydrolase mutant - H-2-H5 complex with (S,S)-cyclohexane-1,2-diol

PDB DOI: https://doi.org/10.2210/pdb5JPU/pdb

Classification: HYDROLASE
Organism(s): Rhodococcus erythropolis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-04 Released: 2016-06-15
Deposition Author(s): Li, G., Zhang, H., Sun, Z., Liu, X., Reetz, M.T.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.246 (Depositor), 0.243 (DCC)
R-Value Work:
0.228 (Depositor), 0.225 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Multi-Parameter Optimization in Directed Evolution: Engineering Thermostability, Enantioselectivity and Activity of an Epoxide Hydrolase

Li, G., Zhang, H., Sun, Z., Liu, X., Reetz, M.T.

To be published.

Macromolecule Content

Total Structure Weight: 35.23 kDa
Atom Count: 2,129
Modeled Residue Count: 236
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
limonene epoxide hydrolase	A, B	155	Rhodococcus erythropolis	Mutation(s): 0 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
3ZQ Query on 3ZQ Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	(1S,2S)-cyclohexane-1,2-diol C₆ H₁₂ O₂ PFURGBBHAOXLIO-WDSKDSINSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.246 (Depositor), 0.243 (DCC)
R-Value Work: 0.228 (Depositor), 0.225 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.539	α = 90
b = 65.539	β = 90
c = 72.857	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-06-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31370925

Revision History (Full details and data files)

Version 1.0: 2016-06-15
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.