Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 45.09 kDa 
• Atom Count: 3278 
• Modelled Residue Count: 261 
• Deposited Residue Count: 274 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2W7N

Crystal Structure of KorA Bound to Operator DNA: Insight into Repressor Cooperation in RP4 Gene Regulation

• PDB DOI: 10.2210/pdb2W7N/pdb
• NDB: NA0248

• Classification: TRANSCRIPTION/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-12-23 Released: 2009-02-17 
• Deposition Author(s): Koenig, B., Mueller, J.J., Lanka, E., Heinemann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.201 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

Crystal Structure of Kora Bound to Operator DNA: Insight Into Repressor Cooperation in Rp4 Gene Regulation

Koenig, B., Mueller, J.J., Lanka, E., Heinemann, U.

(2009) Nucleic Acids Res 37: 1915

• PubMed: 19190096 
• DOI: 10.1093/nar/gkp044
• Primary Citation of Related Structures:  
  2W7N


• PubMed Abstract: 
  

KorA is a global repressor in RP4 which regulates cooperatively the expression of plasmid genes whose products are involved in replication, conjugative transfer and stable inheritance. The structure of KorA bound to an 18-bp DNA duplex that contains the symmetric operator sequence and incorporates 5-bromo-deoxyuridine nucleosides has been determined by multiple-wavelength anomalous diffraction phasing at 1.96-A resolution. KorA is present as a symmetric dimer and contacts DNA via a helix-turn-helix motif. Each half-site of the symmetric operator DNA binds one copy of the protein in the major groove. As confirmed by mutagenesis, recognition specificity is based on two KorA side chains forming hydrogen bonds to four bases within each operator half-site. KorA has a unique dimerization module shared by the RP4 proteins TrbA and KlcB. We propose that these proteins cooperate with the global RP4 repressor KorB in a similar manner via this dimerization module and thus regulate RP4 inheritance.

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Organizational Affiliation: 

Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRFB TRANSCRIPTIONAL REPRESSOR PROTEIN	A, B	101	Escherichia coli	Mutation(s): 0  Gene Names: trfB, korA
UniProt
Find proteins for P03052 (Escherichia coli) Explore P03052  Go to UniProtKB:  P03052

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*TP*GP*TP*TP*TP*AP*GP*CP *TP*AP*AP*AP*CP*AP*AP*G)-3'	C [auth E], E [auth G]	18	Escherichia coli

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*BRUP*BRUP*GP*TP*TP*TP*AP*GP*CP*TP*AP *AP*AP*CP*AP*BRUP*T)-3'	D [auth F], F [auth H]	18	Escherichia coli

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.201 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.83	α = 90
b = 115.45	β = 114
c = 49.88	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
XDS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-12-23 
• Released Date: 2009-02-17 
Deposition Author(s): Koenig, B., Mueller, J.J., Lanka, E., Heinemann, U.

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-05-22
  Changes: Data collection, Derived calculations, Experimental preparation