3R2U | pdb_00003r2u

2.1 Angstrom Resolution Crystal Structure of Metallo-beta-lactamase from Staphylococcus aureus subsp. aureus COL

PDB DOI: https://doi.org/10.2210/pdb3R2U/pdb

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

Deposited: 2011-03-14 Released: 2011-03-23
Deposition Author(s): Minasov, G., Wawrzak, Z., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Kiryukhina, O., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.197 (Depositor), 0.207 (DCC)
R-Value Work:
0.156 (Depositor), 0.169 (DCC)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

2.1 Angstrom Resolution Crystal Structure of Metallo-beta-lactamase Family Protein from Staphylococcus aureus subsp. aureus COL

Minasov, G., Wawrzak, Z., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Kiryukhina, O., Papazisi, L., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 209.23 kDa
Atom Count: 12,459
Modeled Residue Count: 1,359
Deposited Residue Count: 1,864
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase family protein	A, B, C, D	466	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0 Gene Names: SACOL0046
UniProt
Find proteins for A0A0H2X0Y8 (Staphylococcus aureus (strain COL)) Explore A0A0H2X0Y8 Go to UniProtKB: A0A0H2X0Y8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2X0Y8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain J [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D]	E [auth A], F [auth B], J [auth C], M [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain J [auth C] Focus chain M [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	G [auth B], H [auth B], K [auth C], L [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.197 (Depositor), 0.207 (DCC)
R-Value Work: 0.156 (Depositor), 0.169 (DCC)
R-Value Observed: 0.158 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.484	α = 90
b = 92.484	β = 90
c = 385.395	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-03-23

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-03-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations