5EGJ

The structural and biochemical characterization of acyl-coa hydrolase mutant Asn28Ala from Staphylococcus aureus in complex with COENZYME A

PDB DOI: https://doi.org/10.2210/pdb5EGJ/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-10-27 Released: 2015-11-11
Deposition Author(s): Khandokar, Y.B., Srivastava, P.S., Forwood, J.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.257
R-Value Work: 0.207
R-Value Observed: 0.210

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The structural and biochemical characterization of acyl-coa hydrolase from Staphylococcus aureus

Khandokar, Y.B., Srivastava, P.S., Forwood, J.K.

To be published.

Macromolecule Content

Total Structure Weight: 20.99 kDa
Atom Count: 1,374
Modelled Residue Count: 167
Deposited Residue Count: 179
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl CoA Hydrolase	A	179	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 1 Gene Names: SAV1878
UniProt
Find proteins for A0A0H3K033 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Go to UniProtKB: A0A0H3K033
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.257
R-Value Work: 0.207
R-Value Observed: 0.210
Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.73	α = 90
b = 127.73	β = 90
c = 55.722	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-11-11

Deposition Author(s):

Khandokar, Y.B.

Srivastava, P.S.

Revision History (Full details and data files)

Version 1.0: 2015-11-11
Type: Initial release
Version 1.1: 2015-11-25
Changes: Structure summary
Version 1.2: 2015-12-16
Changes: Other
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, 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 R01GM157729.