3P8K | pdb_00003p8k

Crystal Structure of a putative carbon-nitrogen family hydrolase from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb3P8K/pdb

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

Deposited: 2010-10-14 Released: 2011-10-19
Deposition Author(s): Gordon, R.D., Qiu, W., Battaile, K., Lam, K., Soloveychik, M., Benetteraj, D., Romanov, V., Pai, E.F., Chirgadze, N.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.230 (Depositor), 0.235 (DCC)
R-Value Work:
0.197 (Depositor), 0.201 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of carbon-nitrogen family hydrolase from Staphylococcus aureus

Qiu, W., Gordon, R.D., Battaile, K., Lam, K., Soloveychik, M., Benetteraj, D., Romanov, V., Pai, E.F., Chirgadze, N.Y.

To be published.

Macromolecule Content

Total Structure Weight: 65.68 kDa
Atom Count: 4,962
Modeled Residue Count: 536
Deposited Residue Count: 562
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase, carbon-nitrogen family	A, B	281	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0 Gene Names: SACOL2021
UniProt
Find proteins for A0A0H2WXM0 (Staphylococcus aureus (strain COL)) Explore A0A0H2WXM0 Go to UniProtKB: A0A0H2WXM0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2WXM0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain D [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain D [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain D [auth A]	D [auth A], J [auth A], K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain D [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.230 (Depositor), 0.235 (DCC)
R-Value Work: 0.197 (Depositor), 0.201 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.58	α = 90
b = 61.98	β = 90
c = 155.16	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHARP	phasing
BUSTER	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-10-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-19
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary