4WUD

N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from no salt condition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The role of monovalent cations in the ATPase reaction of DNA gyrase

Hearnshaw, S.J.Chung, T.T.Stevenson, C.E.M.Maxwell, A.Lawson, D.M.

(2015) Acta Crystallogr.,Sect.D 71: 996-1005

  • DOI: 10.1107/S1399004715002916
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Four new crystal structures of the ATPase domain of the GyrB subunit of Escherichia coli DNA gyrase have been determined. One of these, solved in the presence of K(+), is the highest resolution structure reported so far for this domain and, in conjun ...

    Four new crystal structures of the ATPase domain of the GyrB subunit of Escherichia coli DNA gyrase have been determined. One of these, solved in the presence of K(+), is the highest resolution structure reported so far for this domain and, in conjunction with the three other structures, reveals new insights into the function of this domain. Evidence is provided for the existence of two monovalent cation-binding sites: site 1, which preferentially binds a K(+) ion that interacts directly with the α-phosphate of ATP, and site 2, which preferentially binds an Na(+) ion and the functional significance of which is not clear. The crystallographic data are corroborated by ATPase data, and the structures are compared with those of homologues to investigate the broader conservation of these sites.


    Organizational Affiliation

    Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
A
392Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: gyrB (acrB, cou, himB, hisU, nalC, parA, pcbA)
EC: 5.6.2.3
Find proteins for P0AES6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AES6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 87.800α = 90.00
b = 141.480β = 90.00
c = 80.300γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references