4EWT

The crystal structure of a putative aminohydrolase from methicillin resistant Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb4EWT/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus COL
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-27 Released: 2013-02-20
Deposition Author(s): Girish, T.S., Vivek, B., Colaco, M., Misquith, S., Gopal, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.229
R-Value Work: 0.199
R-Value Observed: 0.200

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of an amidohydrolase, SACOL0085, from methicillin-resistant Staphylococcus aureus COL

Girish, T.S., Vivek, B., Colaco, M., Misquith, S., Gopal, B.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 103-108

PubMed: 23385746 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309112049822
Primary Citation of Related Structures:
4EWT

PubMed Abstract:
Staphylococcus aureus is an opportunistic pathogen that rapidly acquires resistance to frontline antibiotics. The characterization of novel protein targets from this bacterium is thus an important step towards future therapeutic strategies. Here, the crystal structure of an amidohydrolase, SACOL0085, from S. aureus COL is described. SACOL0085 is a member of the M20D family of peptidases. Unlike other M20D peptidases, which are either monomers or dimers, SACOL0085 adopts a butterfly-shaped homotetrameric arrangement with extensive intersubunit interactions. Each subunit of SACOL0085 contains two Mn(2+) ions at the active site. A conserved cysteine residue at the active site distinguishes M20D peptidases from other M20 family members. This cysteine, Cys103, serves as bidentate ligand coordinating both Mn(2+) ions in SACOL0085.

Organizational Affiliation

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.

Macromolecule Content

Total Structure Weight: 174.18 kDa
Atom Count: 12,344
Modelled Residue Count: 1,542
Deposited Residue Count: 1,568
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase, M20/M25/M40 family	A, B [auth C], C [auth D], D [auth B]	392	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0 Gene Names: SACOL0085 EC: 3.5.1.14
UniProt
Find proteins for A0A0H2WZV8 (Staphylococcus aureus (strain COL)) Explore A0A0H2WZV8 Go to UniProtKB: A0A0H2WZV8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2WZV8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE7 Query on PE7 Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain L [auth D] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain L [auth D] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	L [auth D], O [auth B], P [auth B]	1-DEOXY-1-THIO-HEPTAETHYLENE GLYCOL C₁₄ H₃₀ O₇ S ACMBXVJDKVNCGH-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Focus chain O [auth B] Focus chain P [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	E [auth A] F [auth A] H [auth C] I [auth C] J [auth D] E [auth A], F [auth A], H [auth C], I [auth C], J [auth D], K [auth D], M [auth B], N [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.229
R-Value Work: 0.199
R-Value Observed: 0.200
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.62	α = 115.4
b = 120.11	β = 94.64
c = 132.41	γ = 96.55

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-02-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-02-20
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description