8X6D | pdb_00008x6d

Crystal structure of the C-terminal TBF1

• PDB DOI: https://doi.org/10.2210/pdb8X6D/pdb
• NAKB: 8X6D

• Classification: DNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C, DNA molecule
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-11-21 Released: 2024-11-27 
• Deposition Author(s): Gao, Y., Niu, L.W.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Structural study of yeast TBF1 protein

Gao, Y., Niu, L.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.25 kDa 
• Atom Count: 3,033 
• Modeled Residue Count: 287 
• Deposited Residue Count: 352 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein TBF1	A [auth B], D [auth E], E [auth F]	102	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: TBF1
UniProt
Find proteins for Q02457 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02457  Go to UniProtKB:  Q02457

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')	B [auth C]	23	DNA molecule

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*C)-3')	C [auth D]	23	DNA molecule

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.237 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.794	α = 90
b = 72.103	β = 99.57
c = 63.132	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Gao, Y., Niu, L.W.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release