5EGJ | pdb_00005egj

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 (Depositor), 0.259 (DCC)
R-Value Work:
0.207 (Depositor), 0.210 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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
Modeled Residue Count: 167
Deposited Residue Count: 179
Unique protein chains: 1

Macromolecules

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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)) Explore A0A0H3K033 Go to UniProtKB: A0A0H3K033
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	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] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.257 (Depositor), 0.259 (DCC)
R-Value Work: 0.207 (Depositor), 0.210 (DCC)
R-Value Observed: 0.210 (Depositor)

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

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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

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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.