3PD7 | pdb_00003pd7

Crystal Structure of the Sixth BRCT Domain of Human TopBP1

• PDB DOI: https://doi.org/10.2210/pdb3PD7/pdb
• Entry: 3PD7 supersedes: 3L3E

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-10-22 Released: 2010-12-08 
• Deposition Author(s): Lee, J., Xu, C., Cui, G., Thompson, J.R., Mer, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.144 (Depositor), 0.131 (DCC) 
• R-Value Work: 
  0.114 (Depositor) 
• R-Value Observed: 
  0.114 (Depositor) 

Literature

Crystal Structure of the Sixth BRCT Domain of Human TopBP1

Lee, J., Xu, C., Cui, G., Thompson, J.R., Mer, G.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.43 kDa 
• Atom Count: 2,042 
• Modeled Residue Count: 188 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2-binding protein 1	A, B	107	Homo sapiens	Mutation(s): 1  Gene Names: TOPBP1, KIAA0259
UniProt & NIH Common Fund Data Resources
Find proteins for Q92547 (Homo sapiens) Explore Q92547  Go to UniProtKB:  Q92547
PHAROS:  Q92547 GTEx:  ENSG00000163781

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.144 (Depositor), 0.131 (DCC) 
• R-Value Work:  0.114 (Depositor) 
• R-Value Observed: 0.114 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.877	α = 90
b = 37.911	β = 89.99
c = 79.43	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-08 
Deposition Author(s): Lee, J., Xu, C., Cui, G., Thompson, J.R., Mer, G.
• This entry supersedes: 3L3E

Revision History  

• Version 1.0: 2010-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references