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- PDB-7n5j: PCNA from Thermococcus gammatolerans: crystal I, collection 5, 2.... -

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Basic information

Entry
Database: PDB / ID: 7n5j
TitlePCNA from Thermococcus gammatolerans: crystal I, collection 5, 2.82 A, 89.1 MGy
ComponentsDNA polymerase sliding clamp
KeywordsDNA BINDING PROTEIN / PCNA / sliding clamp / radioresistance / radiation damage / ionizing radiation
Function / homology
Function and homology information


DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / DNA binding
Similarity search - Function
Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / :
Similarity search - Domain/homology
DNA polymerase sliding clamp
Similarity search - Component
Biological speciesThermococcus gammatolerans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsMarin-Tovar, Y. / Rudino-Pinera, E.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN209920 Mexico
CitationJournal: Proteins / Year: 2022
Title: PCNA from Thermococcus gammatolerans: A protein involved in chromosomal DNA metabolism intrinsically resistant at high levels of ionizing radiation.
Authors: Marin-Tovar, Y. / Serrano-Posada, H. / Diaz-Vilchis, A. / Rudino-Pinera, E.
History
DepositionJun 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase sliding clamp
B: DNA polymerase sliding clamp
C: DNA polymerase sliding clamp
D: DNA polymerase sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,15340
Polymers120,7664
Non-polymers3,38736
Water5,765320
1
A: DNA polymerase sliding clamp
B: DNA polymerase sliding clamp
hetero molecules

C: DNA polymerase sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,11730
Polymers90,5753
Non-polymers2,54227
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/21
Buried area10040 Å2
ΔGint-210 kcal/mol
Surface area32620 Å2
MethodPISA
2
D: DNA polymerase sliding clamp
hetero molecules

D: DNA polymerase sliding clamp
hetero molecules

D: DNA polymerase sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,10930
Polymers90,5753
Non-polymers2,53427
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area10250 Å2
ΔGint-182 kcal/mol
Surface area32750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.870, 187.870, 64.314
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
DNA polymerase sliding clamp / Proliferating cell nuclear antigen homolog / PCNA


Mass: 30191.521 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3) (archaea)
Strain: DSM 15229 / JCM 11827 / EJ3 / Gene: pcn, TGAM_1046 / Plasmid: pCold-I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5A5N6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.2
Details: 100 mM sodium citrate pH 5.2, 3.2 M ammonium sulfate, 7.5% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.82→37.33 Å / Num. obs: 31591 / % possible obs: 99.75 % / Redundancy: 10.3 % / CC1/2: 0.979 / Rmerge(I) obs: 0.1524 / Net I/σ(I): 18.68
Reflection shellResolution: 2.82→2.92 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.205 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 3147 / CC1/2: 0.797 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6D

5a6d


Resolution: 2.82→37.326 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 1579 5.01 %
Rwork0.1704 29947 -
obs0.1736 31526 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.64 Å2 / Biso mean: 72.9233 Å2 / Biso min: 36.42 Å2
Refinement stepCycle: final / Resolution: 2.82→37.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7848 0 198 320 8366
Biso mean--105.03 75.58 -
Num. residues----990
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8201-2.9110.31511410.23512710100
2.911-3.0150.29541500.20882664100
3.015-3.13570.25981010.19232745100
3.1357-3.27830.25541440.18622690100
3.2783-3.45110.2541330.16892717100
3.4511-3.66710.2421490.15732730100
3.6671-3.950.25191210.16012729100
3.95-4.34690.18111580.1552715100
4.3469-4.97470.19641560.13632718100
4.9747-6.26280.29411560.1822745100
6.2628-37.3260.21531700.1867278499

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