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- PDB-1isq: Pyrococcus furiosus PCNA complexed with RFCL PIP-box peptide -

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Basic information

Entry
Database: PDB / ID: 1isq
TitlePyrococcus furiosus PCNA complexed with RFCL PIP-box peptide
Components
  • Proliferating Cell Nuclear Antigen
  • replication factor C large subunit
KeywordsDNA BINDING PROTEIN / Toroidal trimer
Function / homology
Function and homology information


DNA clamp loader activity / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Replication factor C, large subunit / RCF1/5-like, AAA+ ATPase lid 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 ...Replication factor C, large subunit / RCF1/5-like, AAA+ ATPase lid 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 / : / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
: / DNA polymerase sliding clamp / Replication factor C large subunit
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMatsumiya, S. / Ishino, S. / Ishino, Y. / Morikawa, K.
CitationJournal: Genes Cells / Year: 2002
Title: Physical interaction between proliferating cell nuclear antigen and replication factor C from Pyrococcus furiosus
Authors: Matsumiya, S. / Ishino, S. / Ishino, Y. / Morikawa, K.
History
DepositionDec 19, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2002Provider: 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 / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proliferating Cell Nuclear Antigen
B: replication factor C large subunit


Theoretical massNumber of molelcules
Total (without water)29,3862
Polymers29,3862
Non-polymers00
Water57632
1
A: Proliferating Cell Nuclear Antigen
B: replication factor C large subunit

A: Proliferating Cell Nuclear Antigen
B: replication factor C large subunit

A: Proliferating Cell Nuclear Antigen
B: replication factor C large subunit


Theoretical massNumber of molelcules
Total (without water)88,1586
Polymers88,1586
Non-polymers00
Water1086
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
Unit cell
Length a, b, c (Å)91.847, 91.847, 64.144
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe second and third parts of the biological assembly are generated by the three-fold axis: -y, x-y, z and y-x+1, -x+1, z.

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Components

#1: Protein Proliferating Cell Nuclear Antigen / DNA POLYMERASE SLIDING CLAMP


Mass: 28018.215 Da / Num. of mol.: 1 / Mutation: M73L
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: Protein/peptide replication factor C large subunit


Mass: 1367.654 Da / Num. of mol.: 1 / Fragment: C-terminal PIP-box region / Source method: obtained synthetically
Details: This sequence corresponds to the residues 469-479 of Pyrococcus furiosus replication factor C large subunit.
References: GenBank: 6539526, UniProt: Q9UWR2*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, sodium citrate, glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.8 mMpeptide1drop
2100 mMsodium citrate1reservoirpH5.5
32.4 Mammonium sulfate1reservoir
410 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Feb 17, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 13871 / Num. obs: 13871 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 41.01 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.32
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.24 / Num. unique all: 1377 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 13867 / Redundancy: 4.4 % / Num. measured all: 60038 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 99.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GE8

1ge8


Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2913 1342 9.73 %random
Rwork0.2348 ---
all-13806 --
obs-13793 99.9 %-
Displacement parametersBiso mean: 38.192 Å2
Baniso -1Baniso -2Baniso -3
1--3.287 Å2-5.475 Å20 Å2
2---3.287 Å20 Å2
3---6.574 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 0 32 1991
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.2733
X-RAY DIFFRACTIONc_dihedral_angle_d25.6853
X-RAY DIFFRACTIONc_improper_angle_d0.7361
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.3119 118 -
Rwork0.2575 --
obs-1355 99.8 %
Refinement
*PLUS
Rfactor Rfree: 0.2913 / Rfactor Rwork: 0.2348
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor Rfree: 0.3119 / Rfactor Rwork: 0.2575

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