3ILW | pdb_00003ilw

Structure of DNA gyrase subunit A N-terminal domain

• PDB DOI: https://doi.org/10.2210/pdb3ILW/pdb

• Classification: ISOMERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-07 Released: 2009-10-06 
• Deposition Author(s): Tretter, E.M., Schoeffler, A.J., Weisfield, S.R., Berger, J.M., TB Structural Genomics Consortium (TBSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.201 (Depositor) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the DNA gyrase GyrA N-terminal domain from Mycobacterium tuberculosis.

Tretter, E.M., Schoeffler, A.J., Weisfield, S.R., Berger, J.M.

(2010) Proteins 78: 492-495

• PubMed: 19787774 
• DOI: https://doi.org/10.1002/prot.22600
• Primary Citation Related Structures: 
  3ILW

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Organizational Affiliation: 
• Division of Biochemistry and Molecular Biology, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720-3220, 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: 105.34 kDa 
• Atom Count: 8,027 
• Modeled Residue Count: 927 
• Deposited Residue Count: 940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit A	A, B	470	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: gyrA, MT0006, MTCY10H4.04, Rv0006 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P9WG47 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG47  Go to UniProtKB:  P9WG47

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.201 (Depositor) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.228	α = 109.96
b = 70.054	β = 91.16
c = 97.812	γ = 114.16

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Tretter, E.M., Schoeffler, A.J., Weisfield, S.R., Berger, J.M., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2023-09-06
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description