1KU9

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)

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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) 

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 
• DOI: https://doi.org/10.1002/prot.10272
• Primary Citation of Related Structures:  
  1KU9

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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