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- PDB-6aig: Crystal structure of PCNA1 from Aeropyrum pernix -

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Basic information

Entry
Database: PDB / ID: 6aig
TitleCrystal structure of PCNA1 from Aeropyrum pernix
ComponentsDNA polymerase sliding clamp 1
KeywordsREPLICATION / Monomer
Function / homology
Function and homology information


DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / DNA binding
Similarity search - Function
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 / :
Similarity search - Domain/homology
DNA polymerase sliding clamp 1
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYamauchi, T. / Kikuchi, M. / Tsunoda, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2024
Title: X-ray crystal structure of proliferating cell nuclear antigen 1 from Aeropyrum pernix.
Authors: Yamauchi, T. / Kikuchi, M. / Iizuka, Y. / Tsunoda, M.
History
DepositionAug 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Refinement description / Category: database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _software.version
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase sliding clamp 1


Theoretical massNumber of molelcules
Total (without water)29,4801
Polymers29,4801
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12700 Å2
Unit cell
Length a, b, c (Å)69.028, 69.028, 120.857
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 DNA polymerase sliding clamp 1 / Proliferating cell nuclear antigen


Mass: 29479.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Strain: K1 / Gene: APE_0162 / Plasmid: pET-11a / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9YFT8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: McIlvaine buffer, Lithium Sulfate, isoPropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 10, 2018
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→48.86 Å / Num. obs: 20195 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.019 / Rrim(I) all: 0.051 / Χ2: 1.01 / Net I/σ(I): 34.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 15 / Num. unique obs: 1476 / CC1/2: 0.993 / Rpim(I) all: 0.067 / Rrim(I) all: 0.177 / Χ2: 0.82 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSVERSION Nov 11, 2017data reduction
XDSVERSION Nov 11,2017data scaling
MOLREPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IZ4

1iz4


Resolution: 2→48.86 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.353 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22552 991 4.8 %RANDOM
Rwork0.18505 ---
obs0.18709 19446 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.646 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 0 63 2022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0142018
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171912
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.6542743
X-RAY DIFFRACTIONr_angle_other_deg1.0021.6324445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8425267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.70219.89595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10915353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3761519
X-RAY DIFFRACTIONr_chiral_restr0.0810.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8912.5951041
X-RAY DIFFRACTIONr_mcbond_other2.8852.5921040
X-RAY DIFFRACTIONr_mcangle_it4.0743.8731302
X-RAY DIFFRACTIONr_mcangle_other4.0733.8761303
X-RAY DIFFRACTIONr_scbond_it4.163.121975
X-RAY DIFFRACTIONr_scbond_other4.1583.123976
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4014.4561437
X-RAY DIFFRACTIONr_long_range_B_refined7.97630.8852098
X-RAY DIFFRACTIONr_long_range_B_other7.97330.8072088
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 69 -
Rwork0.196 1403 -
obs--99.93 %

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