4YHR | pdb_00004yhr

Crystal Structure of Yeast Proliferating Cell Nuclear Antigen

• PDB DOI: https://doi.org/10.2210/pdb4YHR/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-27 Released: 2015-03-18 
• Deposition Author(s): Litman, J.M., Nguyen, V.Q., Kondratick, C.M., Powers, K.T., Schnieders, M.J., Washington, M.T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

Dead-End Elimination with a Polarizable Force Field Repacks PCNA Models from Low-Resolution X-ray Diffraction into Atomic Resolution Structures

LuCore, S.D., Litman, J.M., Powers, K.T., Lynn, A.M., Tollefsen, W.T.A., Fenn, T.D., Washington, M.T., Schnieders, M.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.04 kDa 
• Atom Count: 2,011 
• Modeled Residue Count: 256 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	A	266	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: POL30, YBR088C, YBR0811
UniProt
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P15873  Go to UniProtKB:  P15873

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.259	α = 90
b = 124.259	β = 90
c = 124.259	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Litman, J.M., Nguyen, V.Q., Kondratick, C.M., Powers, K.T., Schnieders, M.J., Washington, M.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008365

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
• Version 1.2: 2017-11-22
  Changes: Database references, Refinement description
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description