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- PDB-7n5n: PCNA from Thermococcus gammatolerans: crystal III, collection 15,... -

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Basic information

Entry
Database: PDB / ID: 7n5n
TitlePCNA from Thermococcus gammatolerans: crystal III, collection 15, 2.20 A, 28.7 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 / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / 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: 2.2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,88818
Polymers60,3832
Non-polymers1,50516
Water2,252125
1
A: DNA polymerase sliding clamp
hetero molecules

A: DNA polymerase sliding clamp
hetero molecules

A: DNA polymerase sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,12130
Polymers90,5753
Non-polymers2,54627
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area9470 Å2
ΔGint-210 kcal/mol
Surface area32270 Å2
MethodPISA
2
B: DNA polymerase sliding clamp
hetero molecules

B: DNA polymerase sliding clamp
hetero molecules

B: DNA polymerase sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,54424
Polymers90,5753
Non-polymers1,97021
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8500 Å2
ΔGint-119 kcal/mol
Surface area32860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.056, 93.056, 63.976
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

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Components

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


Mass: 30191.521 Da / Num. of mol.: 2
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.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.65 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.2
Details: 100 mM sodium citrate pH 5.2, 3.0 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: 2.2→34.095 Å / Num. obs: 31432 / % possible obs: 99.62 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1307 / Net I/σ(I): 19.02
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 3150 / CC1/2: 0.748 / % possible all: 99.75

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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: 2.2→34.095 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2257 1564 4.98 %
Rwork0.1765 29816 -
obs0.1788 31380 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.75 Å2 / Biso mean: 60.8378 Å2 / Biso min: 34.55 Å2
Refinement stepCycle: final / Resolution: 2.2→34.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 88 125 4137
Biso mean--85.83 62.56 -
Num. residues----495
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2710.32521290.25392760100
2.271-2.35220.27811390.24882702100
2.3522-2.44630.26461380.23252721100
2.4463-2.55760.2921520.2183269499
2.5576-2.69240.2641680.20762677100
2.6924-2.8610.2311560.18522668100
2.861-3.08180.22631410.19042732100
3.0818-3.39170.2761420.1853270599
3.3917-3.88190.21081470.15572713100
3.8819-4.88840.18081280.1462272499
4.8884-34.0950.21671240.17752720100

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