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- PDB-1iz4: Pyrococcus furiosus PCNA mutant (Met73Leu/Asp143Ala): tetragonal form -

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Basic information

Entry
Database: PDB / ID: 1iz4
TitlePyrococcus furiosus PCNA mutant (Met73Leu/Asp143Ala): tetragonal 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: 2 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 21, 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 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.5Oct 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

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)27,9741
Polymers27,9741
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.994, 64.994, 156.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 27974.205 Da / Num. of mol.: 1 / Mutation: M73L, D143A
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.: 42 / 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: 3.05 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: ammonium sulfate, sodium citrate, glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium citrate1reservoirpH4.5
20.6 Mammonium sulfate1reservoir
340 %(v/v)D143A1reservoir

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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 14, 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: 2→35 Å / Num. all: 22362 / Num. obs: 22310 / % possible obs: 95.9 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Biso Wilson estimate: 38.25 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.06 / Net I/σ(I): 10
Reflection shellResolution: 2→2.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3243 / Rsym value: 0.459 / % possible all: 97.4
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. measured all: 91731
Reflection shell
*PLUS
% possible obs: 97.4 %

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Processing

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

1ge8


Resolution: 2→35 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2986 2211 -Random
Rwork0.2698 ---
all-22295 --
obs-22295 94.9 %-
Displacement parametersBiso mean: 29.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.362 Å2-1.362 Å22.725 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 0 42 1936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006089
X-RAY DIFFRACTIONc_angle_deg1.24735
X-RAY DIFFRACTIONc_dihedral_angle_d25.49287
X-RAY DIFFRACTIONc_improper_angle_d0.70793
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection
Rfree0.2934 206
Rwork0.2665 -
obs-2220
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 35 Å / Num. reflection obs: 20084
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00609
X-RAY DIFFRACTIONc_angle_deg1.247
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.708

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