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- PDB-7n5i: PCNA from Thermococcus gammatolerans: crystal I, collection 1, 1.... -

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Basic information

Entry
Database: PDB / ID: 7n5i
TitlePCNA from Thermococcus gammatolerans: crystal I, collection 1, 1.95 A, 5.22 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: 1.95 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 area9880 Å2
ΔGint-216 kcal/mol
Surface area32100 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 area9960 Å2
ΔGint-192 kcal/mol
Surface area32350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.616, 186.616, 63.918
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: 2.66 Å3/Da / Density % sol: 54 %
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: 1.95→32.323 Å / Num. obs: 92797 / % possible obs: 99.89 % / Redundancy: 10.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.189 / Net I/σ(I): 27.82
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.003 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 9191 / CC1/2: 0.886 / % possible all: 99.83

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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: 1.95→32.323 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 4699 5.07 %
Rwork0.1914 88026 -
obs0.1932 92725 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.67 Å2 / Biso mean: 45.7013 Å2 / Biso min: 22.27 Å2
Refinement stepCycle: final / Resolution: 1.95→32.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7848 0 198 320 8366
Biso mean--71.04 47.81 -
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 (%)
1.95-1.97220.28651710.26642866100
1.9722-1.99540.30321720.25562912100
1.9954-2.01970.25291320.25092929100
2.0197-2.04530.35381110.2512953100
2.0453-2.07220.2891460.25042955100
2.0722-2.10060.29681270.23442926100
2.1006-2.13060.26221630.23692901100
2.1306-2.16230.28931560.22942906100
2.1623-2.19610.25121490.22172970100
2.1961-2.23210.28111830.21912853100
2.2321-2.27060.27261610.22412943100
2.2706-2.31190.26861570.22752891100
2.3119-2.35630.2631610.2162955100
2.3563-2.40440.2581270.21062932100
2.4044-2.45670.25381670.21322951100
2.4567-2.51380.2581630.22272869100
2.5138-2.57670.27331510.22152954100
2.5767-2.64630.25021710.21332903100
2.6463-2.72410.25611350.20552963100
2.7241-2.8120.23691710.19812902100
2.812-2.91240.27851380.2072998100
2.9124-3.0290.22451450.21092924100
3.029-3.16670.25961670.20262921100
3.1667-3.33350.23611350.18822980100
3.3335-3.54210.1951510.1752950100
3.5421-3.81520.19151820.17112927100
3.8152-4.19840.20751650.16182949100
4.1984-4.80420.16941680.14172964100
4.8042-6.04630.21871890.17172945100
6.0463-32.3230.20571850.2007303499

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