6K5U | pdb_00006k5u

Crystal structure of the myb domain of S. pombe Tbf1

• PDB DOI: https://doi.org/10.2210/pdb6K5U/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Schizosaccharomyces pombe 972h-
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-05-31 Released: 2020-06-03 
• Deposition Author(s): Zhou, Y.Z., Wang, N.N., Zhao, Y.C., Zeng, Z.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal structure of the myb domain of S. pombe Tbf1

Zhou, Y.Z., Wang, N.N., Zhao, Y.C., Zeng, Z.X.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.23 kDa 
• Atom Count: 1,365 
• Modeled Residue Count: 156 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Telomeric DNA-binding factor trf1	A, B	79	Schizosaccharomyces pombe 972h-	Mutation(s): 1  Gene Names: trf1, SPBC19G7.13
UniProt
Find proteins for Q6E434 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q6E434  Go to UniProtKB:  Q6E434

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.222 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.393	α = 90
b = 105.393	β = 90
c = 41.302	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Zhou, Y.Z., Wang, N.N., Zhao, Y.C., Zeng, Z.X.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary