1KU9 | pdb_00001ku9

X-ray Structure of a Methanococcus jannaschii DNA-Binding Protein: Implications for Antibiotic Resistance in Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb1KU9/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Methanocaldococcus jannaschii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2002-01-21 Released: 2002-12-25
Deposition Author(s): Ray, S.S., Bonanno, J.B., Chen, H., de Lencastre, H., Wu, S., Tomasz, A., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.280 (Depositor)
R-Value Work:
0.241 (Depositor)
R-Value Observed:
0.245 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1KU9

This is version 1.5 of the entry. See complete history.

Literature

X-ray structure of an M. jannaschii DNA-binding protein: implications for antibiotic resistance in S. aureus

Ray, S.S., Bonanno, J.B., Chen, H., de Lencastre, H., Wu, S., Tomasz, A., Burley, S.K.

(2002) Proteins 50: 170-173

PubMed: 12471609 Search on PubMed
DOI: https://doi.org/10.1002/prot.10272
Primary Citation Related Structures:
1KU9

Organizational Affiliation

Laboratory of Molecular Biophysics, Rockefeller University, New York, New York 10021, USA.

Macromolecule Content

Total Structure Weight: 35.75 kDa
Atom Count: 2,538
Modeled Residue Count: 302
Deposited Residue Count: 304
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein MJ223	A, B	152	Methanocaldococcus jannaschii	Mutation(s): 5 Gene Names: Mj223
UniProt
Find proteins for Q58958 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58958 Go to UniProtKB: Q58958
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58958
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.80 Å
R-Value Free: 0.280 (Depositor)
R-Value Work: 0.241 (Depositor)
R-Value Observed: 0.245 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.939	α = 90
b = 56.939	β = 90
c = 209.515	γ = 120

Software Package:

Software Name	Purpose
MARMAD	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
MLPHARE	phasing
DM	model building
CNS	refinement
MARMAD	data reduction
DM	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2002-12-25

Deposition Author(s):

de Lencastre, H.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2002-12-25
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-10-30
Changes: Data collection, Database references, 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.