7C4Q | pdb_00007c4q

Crystal structure of DBD plasma treated zebrafish TRF2 myb-domain complexed with DNA

• PDB DOI: https://doi.org/10.2210/pdb7C4Q/pdb
• NAKB: 7C4Q

• Classification: DNA BINDING PROTEIN
• Organism(s): Danio rerio, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-18 Released: 2021-05-26 
• Deposition Author(s): Jin, Z., Park, J.H., Yun, J.H., Park, S.Y., Lee, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of DBD plasma treated zebrafish TRF2 myb-domain complexed with DNA

Jin, Y., Park, J.H., Yun, J.H., Park, S.Y., Lee, W.

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 Evidence: gel filtration

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: 27.13 kDa 
• Atom Count: 1,864 
• Modeled Residue Count: 155 
• Deposited Residue Count: 155 
• Unique protein chains: 2
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Terfa protein	A	54	Danio rerio	Mutation(s): 0  Gene Names: terfa
UniProt
Find proteins for Q4FZZ9 (Danio rerio) Explore Q4FZZ9  Go to UniProtKB:  Q4FZZ9

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Terfa protein	D [auth B]	55	Danio rerio	Mutation(s): 0  Gene Names: terfa
UniProt
Find proteins for Q4FZZ9 (Danio rerio) Explore Q4FZZ9  Go to UniProtKB:  Q4FZZ9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')	B [auth C]	12	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')	C [auth D], F	12	Homo sapiens

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')	E	10	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.211	α = 90
b = 64.211	β = 90
c = 143.706	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Jin, Z., Park, J.H., Yun, J.H., Park, S.Y., Lee, W.

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description