3PX7

Crystal Structure of covalent complex of topoisomerase 1A with substrate

• PDB DOI: https://doi.org/10.2210/pdb3PX7/pdb
• NAKB: 3PX7

• Classification: ISOMERASE/DNA
• Organism(s): Escherichia coli DH1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-12-09 Released: 2011-04-20 
• Deposition Author(s): Zhang, Z., Tse-dinh, Y.C., Cheng, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.269 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Structure of E. coli Topoisomerase I Trapped as Covalent Complex Intermediate with Cleaved DNA

Tse-Dinh, Y.C., Zhang, Z., Cheng, B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.86 kDa 
• Atom Count: 4,726 
• Modelled Residue Count: 561 
• Deposited Residue Count: 608 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase	A	595	Escherichia coli DH1	Mutation(s): 1  Gene Names: 415337, EcDH1_2375 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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA 5'-D(*TP*TP*GP*GP*G)-3'	B	5	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA 5'-D(*A*AP*TP*GP*CP*GP*CP*T)-3'	C	8	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	D [auth A], E [auth B], F [auth C]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.269 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.602	α = 90
b = 91.759	β = 90
c = 141.976	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
HKL-3000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-20 
Deposition Author(s): Zhang, Z., Tse-dinh, Y.C., Cheng, B.

Revision History  

• Version 1.0: 2011-04-20
  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: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary