4WUB

N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from 100 mM KCl condition

• PDB DOI: https://doi.org/10.2210/pdb4WUB/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-31 Released: 2015-04-08 
• Deposition Author(s): Hearnshaw, S.J., Chung, T.T., Stevenson, C.E.M., Maxwell, A., Lawson, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Starting Model: experimental

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 D Biol Crystallogr 71: 996-1005

• PubMed: 25849408 
• DOI: https://doi.org/10.1107/S1399004715002916
• Primary Citation of Related Structures:  
  4WUB, 4WUC, 4WUD, 4XTJ


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.94 kDa 
• Atom Count: 3,240 
• Modelled Residue Count: 384 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A	392	Escherichia coli K-12	Mutation(s): 0  Gene Names: gyrB, acrB, himB, hisU, nalC, parA, pcbA, b3699, JW5625 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0AES6 (Escherichia coli (strain K12)) Explore P0AES6  Go to UniProtKB:  P0AES6

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.88	α = 90
b = 140.9	β = 90
c = 79.56	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Hearnshaw, S.J., Chung, T.T., Stevenson, C.E.M., Maxwell, A., Lawson, D.M.

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Database references
• Version 1.2: 2015-08-19
  Changes: Derived calculations
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description