5CW2 | pdb_00005cw2

Crystal structure of Epoxide Hydrolase A from Mycobacterium thermoresistibile

PDB DOI: https://doi.org/10.2210/pdb5CW2/pdb

Classification: HYDROLASE
Organism(s): Mycolicibacterium thermoresistibile ATCC 19527
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-27 Released: 2016-08-17
Deposition Author(s): Schulz, E.C., Wilmanns, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.251 (Depositor), 0.245 (DCC)
R-Value Work:
0.209 (Depositor), 0.208 (DCC)
R-Value Observed:
0.213 (Depositor)

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Ligand Structure Quality Assessment

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Literature

The crystal structure of mycobacterial Epoxide Hydrolase A

Schulz, E.C., Wilmanns, M., Henderson, S., Southall, S.

To be published.

Macromolecule Content

Total Structure Weight: 143.18 kDa
Atom Count: 10,371
Modeled Residue Count: 1,276
Deposited Residue Count: 1,300
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative epoxide hydrolase EPHA	A [auth C], B [auth A], C [auth B], D	325	Mycolicibacterium thermoresistibile ATCC 19527	Mutation(s): 0 Gene Names: KEK_07967 EC: 3.3.2.3
UniProt
Find proteins for G7CF24 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)) Explore G7CF24 Go to UniProtKB: G7CF24
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G7CF24
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BSU Query on BSU Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth D] SDF format, chain G [auth B] SDF format, chain E [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth B] MOL2 format, chain E [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth B] mmCIF format, chain E [auth C]	E [auth C], F [auth A], G [auth B], H [auth D]	1,3-DIPHENYLUREA C₁₃ H₁₂ N₂ O GWEHVDNNLFDJLR-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth D] MOL2 format, chain I [auth D] mmCIF format, chain I [auth D]	I [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.251 (Depositor), 0.245 (DCC)
R-Value Work: 0.209 (Depositor), 0.208 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.8	α = 90
b = 105.01	β = 90.11
c = 108.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-08-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-08-17
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations

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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.