3KOR | pdb_00003kor

Crystal structure of a putative Trp repressor from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb3KOR/pdb

Classification: TRANSCRIPTION
Organism(s): Staphylococcus aureus subsp. aureus USA300_TCH1516
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-11-13 Released: 2010-11-17
Deposition Author(s): Lam, R., Vodsedalek, J., Lam, K., Romanov, V., Battaile, K.P., Beletskaya, I., Pai, E.F., Chirgadze, N.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.221 (Depositor), 0.226 (DCC)
R-Value Work:
0.191 (Depositor), 0.194 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative Trp repressor from Staphylococcus aureus

Lam, R., Vodsedalek, J., Lam, K., Romanov, V., Battaile, K.P., Beletskaya, I., Pai, E.F., Chirgadze, N.Y.

To be published.

Macromolecule Content

Total Structure Weight: 55.19 kDa
Atom Count: 3,543
Modeled Residue Count: 401
Deposited Residue Count: 476
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Possible Trp repressor	A, B, C, D	119	Staphylococcus aureus subsp. aureus USA300_TCH1516	Mutation(s): 0 Gene Names: USA300HOU_1908
UniProt
Find proteins for A0A0H2XJM3 (Staphylococcus aureus (strain USA300)) Explore A0A0H2XJM3 Go to UniProtKB: A0A0H2XJM3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2XJM3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.221 (Depositor), 0.226 (DCC)
R-Value Work: 0.191 (Depositor), 0.194 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.973	α = 90
b = 68.461	β = 96.86
c = 73.17	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-11-17

Deposition Author(s):

Chirgadze, N.Y.

Revision History (Full details and data files)

Version 1.0: 2010-11-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.