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- PDB-3hi8: Crystal structure of proliferating cell nuclear antigen (PCNA) fr... -

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Basic information

Entry
Database: PDB / ID: 3hi8
TitleCrystal structure of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii
ComponentsProliferating cell nuclear antigen PcnA
KeywordsREPLICATION / sliding clamp / DNA interaction / haloferax volcanii
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 speciesHaloferax volcanii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.202 Å
AuthorsMorgunova, E. / Gray, F.C. / MacNeill, S.A. / Ladenstein, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structural insights into the adaptation of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii to a high-salt environment.
Authors: Morgunova, E. / Gray, F.C. / Macneill, S.A. / Ladenstein, R.
History
DepositionMay 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen PcnA
B: Proliferating cell nuclear antigen PcnA
C: Proliferating cell nuclear antigen PcnA
D: Proliferating cell nuclear antigen PcnA
E: Proliferating cell nuclear antigen PcnA
F: Proliferating cell nuclear antigen PcnA


Theoretical massNumber of molelcules
Total (without water)160,1766
Polymers160,1766
Non-polymers00
Water55831
1
A: Proliferating cell nuclear antigen PcnA
B: Proliferating cell nuclear antigen PcnA
C: Proliferating cell nuclear antigen PcnA


Theoretical massNumber of molelcules
Total (without water)80,0883
Polymers80,0883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-13.4 kcal/mol
Surface area34810 Å2
MethodPISA
2
D: Proliferating cell nuclear antigen PcnA
E: Proliferating cell nuclear antigen PcnA
F: Proliferating cell nuclear antigen PcnA


Theoretical massNumber of molelcules
Total (without water)80,0883
Polymers80,0883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-13.1 kcal/mol
Surface area34830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.443, 123.236, 123.256
Angle α, β, γ (deg.)90.000, 135.000, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Proliferating cell nuclear antigen PcnA


Mass: 26695.994 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax volcanii (archaea) / Strain: DS70 / Gene: HVO_0175 / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: D0VWY8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 4M Sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 9, 2007 / Details: Pt coated mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Number: 144482 / Rmerge(I) obs: 0.115 / Χ2: 0.88 / D res high: 2.99 Å / D res low: 30 Å / Num. obs: 37747 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
8.073099.410.0510.2253.7
6.428.0799.910.0950.6893.8
5.626.4210010.1561.1953.9
5.115.6210010.1641.1653.9
4.745.1110010.1711.3143.9
4.464.7410010.2140.9713.9
4.244.4610010.3361.0973.9
4.064.2410010.5120.7623.9
3.94.0610010.8040.7863.9
3.773.910010.7773.9
3.653.7710010.8023.9
3.543.6510010.8173.9
3.453.5410010.7993.9
3.373.4599.910.8033.9
3.293.3710010.873.9
3.223.2910010.9143.9
3.163.2210010.9163.9
3.13.1610010.8673.8
3.043.110010.9483.8
2.993.0486.810.6863.3
ReflectionResolution: 3.2→32.949 Å / Num. obs: 26380 / % possible obs: 99.3 % / Redundancy: 2.2 % / Biso Wilson estimate: 138 Å2 / Rsym value: 0.115 / Net I/σ(I): 4.4
Reflection shellResolution: 3.2→3.36 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.02 / Rsym value: 0.25 / % possible all: 86.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RWZ

1rwz


Resolution: 3.202→32.949 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.787 / Cross valid method: THROUGHOUT / Stereochemistry target values: twin_lsq_f
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1323 5.02 %random
Rwork0.237 ---
obs-26374 86.63 %-
Solvent computationBsol: 60.326 Å2 / ksol: 0.215 e/Å3
Displacement parametersBiso max: 259.96 Å2 / Biso mean: 139.842 Å2 / Biso min: 13.52 Å2
Baniso -1Baniso -2Baniso -3
1-3.812 Å20 Å22.153 Å2
2---1.261 Å20 Å2
3----2.551 Å2
Refinement stepCycle: LAST / Resolution: 3.202→32.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11214 0 0 31 11245
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.4950
X-RAY DIFFRACTIONf_bond_d0.010
X-RAY DIFFRACTIONf_chiral_restr0.0710
X-RAY DIFFRACTIONf_dihedral_angle_d13.0290
X-RAY DIFFRACTIONf_plane_restr0.0050
X-RAY DIFFRACTIONf_nbd_refined4.0420

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