3PWT | pdb_00003pwt

Crystal structure of mutant E.coli topoisomerase IA

• PDB DOI: https://doi.org/10.2210/pdb3PWT/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2010-12-08 Released: 2010-12-29 
• Deposition Author(s): Zhang, Z., Bokun, C., Tse-Dinh, Y.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.249 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 

Literature

Crystal structure of mutant E.coli topoisomerase IA

Zhang, Z., Cheng, B., Tse-Dinh, Y.-C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 67.57 kDa 
• Atom Count: 4,918 
• Modeled Residue Count: 562 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase	A	596	Escherichia coli K-12	Mutation(s): 1  Gene Names: topA, supX, b1274, JW1266 EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt
Find proteins for P06612 (Escherichia coli (strain K12)) Explore P06612  Go to UniProtKB:  P06612

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.249 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.493	α = 90
b = 79.263	β = 90
c = 141.013	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-29 
Deposition Author(s): Zhang, Z., Bokun, C., Tse-Dinh, Y.-C.

Revision History  

• Version 1.0: 2010-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations