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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.273 (Depositor), 0.279 (DCC)
R-Value Work:
0.246 (Depositor)
R-Value Observed:
0.248 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4YHR

This is version 1.4 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15873
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.273 (Depositor), 0.279 (DCC)
R-Value Work: 0.246 (Depositor)
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

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-03-18

Deposition Author(s):

Kondratick, C.M.

Schnieders, M.J.

Washington, M.T.

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.