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- PDB-5auj: Pyrococcus furiosus proliferating cell nuclear antigen (PCNA) SeM... -

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Basic information

Entry
Database: PDB / ID: 5auj
TitlePyrococcus furiosus proliferating cell nuclear antigen (PCNA) SeMet derivative
ComponentsDNA polymerase sliding clamp
KeywordsDNA BINDING PROTEIN / Replication / Processivity / Sliding clamp
Function / homology
Function and homology information


DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / DNA binding
Similarity search - Function
Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 / : / Alpha Beta
Similarity search - Domain/homology
DNA polymerase sliding clamp
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsWatanabe, Y. / Oyama, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology26440023 Japan
CitationJournal: To Be Published
Title: Pyrococcus furiosus proliferating cell nuclear antigen (PCNA) SeMet derivative
Authors: Watanabe, Y. / Oyama, T.
History
DepositionApr 21, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: diffrn_source / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_ref_seq_dif.details
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase sliding clamp


Theoretical massNumber of molelcules
Total (without water)28,4401
Polymers28,4401
Non-polymers00
Water37821
1
A: DNA polymerase sliding clamp

A: DNA polymerase sliding clamp

A: DNA polymerase sliding clamp


Theoretical massNumber of molelcules
Total (without water)85,3213
Polymers85,3213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area4180 Å2
ΔGint-13 kcal/mol
Surface area31170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.545, 88.545, 62.726
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 28440.270 Da / Num. of mol.: 1 / Mutation: M73L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: DSM 3638 / Gene: pcn, PF0983 / Production host: Escherichia coli (E. coli) / References: UniProt: O73947
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.72 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, 1,4-dioxane, sodium citrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19578 / % possible obs: 100 % / Redundancy: 20 % / Net I/σ(I): 18.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→36.17 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.65 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS AND F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2734 922 4.83 %Random
Rwork0.2177 ---
obs0.2203 19090 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 0 21 1871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021874
X-RAY DIFFRACTIONf_angle_d0.4762526
X-RAY DIFFRACTIONf_dihedral_angle_d11.684707
X-RAY DIFFRACTIONf_chiral_restr0.02304
X-RAY DIFFRACTIONf_plane_restr0.002319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4983-2.630.26811200.26632620X-RAY DIFFRACTION100
2.63-2.79470.37561490.26352570X-RAY DIFFRACTION100
2.7947-3.01040.28861270.26612630X-RAY DIFFRACTION100
3.0104-3.31320.29741380.24482555X-RAY DIFFRACTION100
3.3132-3.79220.26371230.20272604X-RAY DIFFRACTION100
3.7922-4.7760.21451330.17532591X-RAY DIFFRACTION100
4.776-100.28391320.2092598X-RAY DIFFRACTION100

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