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- PDB-1iz5: Pyrococcus furiosus PCNA mutant (Met73Leu, Asp143Ala, Asp147Ala):... -

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Basic information

Entry
Database: PDB / ID: 1iz5
TitlePyrococcus furiosus PCNA mutant (Met73Leu, Asp143Ala, Asp147Ala): orthorhombic form
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / DNA / REPLICATION / PROCESSIVITY / SLIDING CLAMP
Function / homology
Function and homology information


DNA polymerase processivity factor activity / leading strand elongation / regulation of 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 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMatsumiya, S. / Ishino, S. / Ishino, Y. / Morikawa, K.
CitationJournal: PROTEIN SCI. / Year: 2003
Title: Intermolecular ion pairs maintain the toroidal structure of Pyrococcus furiosus PCNA
Authors: Matsumiya, S. / Ishino, S. / Ishino, Y. / Morikawa, K.
History
DepositionSep 23, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)55,8602
Polymers55,8602
Non-polymers00
Water2,720151
1
A: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)27,9301
Polymers27,9301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)27,9301
Polymers27,9301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.289, 85.348, 118.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27930.195 Da / Num. of mol.: 2 / Mutation: M73L, D143A, D147A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pET-21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O73947
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.95 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, 2-methyl-2,4-pentanediol, sodium citrate, glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium citrate1reservoirpH5.5
22.6 Mammonium sulfate1reservoir
311 %(v/v)MPD1reservoir
44 %(v/v)glycerol1reservoir
5D143A/D147A1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 13, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.836 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / Num. all: 60694 / Num. obs: 60694 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 33.78 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.073 / Net I/σ(I): 4.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 1.4 / Num. unique all: 8697 / Rsym value: 0.5 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 214024
Reflection shell
*PLUS
% possible obs: 98.8 % / Redundancy: 6.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GE8

1ge8


Resolution: 1.8→35 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2994 5952 -random
Rwork0.2725 ---
all-60915 --
obs-60499 99.3 %-
Displacement parametersBiso mean: 33.3044 Å2
Baniso -1Baniso -2Baniso -3
1-7.844 Å2-14.668 Å26.824 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 1.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 0 151 3919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005983
X-RAY DIFFRACTIONc_angle_deg1.19837
X-RAY DIFFRACTIONc_dihedral_angle_d25.35541
X-RAY DIFFRACTIONc_improper_angle_d0.71484
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.4499 534 -
Rwork0.4344 --
obs-5786 96.37 %
Refinement
*PLUS
Num. reflection obs: 54547 / Rfactor Rfree: 0.2975 / Rfactor Rwork: 0.2715
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00598
X-RAY DIFFRACTIONc_angle_deg1.198
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.715

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