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- PDB-7o1e: Crystal structure of PCNA from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 7o1e
TitleCrystal structure of PCNA from Chaetomium thermophilum
ComponentsProliferating cell nuclear antigen
KeywordsREPLICATION / PCNA / DNA clamp / DNA replication / PIP / homotrimer
Function / homology
Function and homology information


PCNA complex / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / DNA binding
Similarity search - Function
Proliferating cell nuclear antigen signature 2. / 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
Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.34 Å
AuthorsAlphey, M.A. / MacNeill, S. / Yang, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateRIG70668 United Kingdom
CitationJournal: Febs J. / Year: 2023
Title: Non-canonical binding of the Chaetomium thermophilum PolD4 N-terminal PIP motif to PCNA involves Q-pocket and compact 2-fork plug interactions but no 3 10 helix.
Authors: Yang, D. / Alphey, M.S. / MacNeill, S.A.
History
DepositionMar 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 11, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 31, 2024Group: 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)28,7571
Polymers28,7571
Non-polymers00
Water75742
1
A: Proliferating cell nuclear antigen

A: Proliferating cell nuclear antigen

A: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)86,2703
Polymers86,2703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)86.270, 86.270, 90.842
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Proliferating cell nuclear antigen


Mass: 28756.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 3 residues are a linker to the cleaved His-Tag. Flexible loops and sidechains have been omitted or truncated
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0061010
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: G0SF70
#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: 2.26 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M PTCP pH 5.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.34→30.28 Å / Num. obs: 10552 / % possible obs: 98.9 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.046 / Rrim(I) all: 0.108 / Net I/σ(I): 9.6 / Num. measured all: 54849 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.34-2.423.70.54735639510.7860.320.637290.7
9.05-30.285.50.04910021820.9980.0230.05520.497.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TUP

5tup


Resolution: 2.34→30.28 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2813 / WRfactor Rwork: 0.2138 / FOM work R set: 0.7268 / SU B: 24.241 / SU ML: 0.265 / SU R Cruickshank DPI: 0.4532 / SU Rfree: 0.2916 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.453 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2798 544 5.2 %RANDOM
Rwork0.2127 ---
obs0.2161 9986 98.96 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.41 Å2 / Biso mean: 45.245 Å2 / Biso min: 28.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20.66 Å20 Å2
2--1.32 Å20 Å2
3----4.28 Å2
Refinement stepCycle: final / Resolution: 2.34→30.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 0 42 1899
Biso mean---45.12 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131878
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171778
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.632542
X-RAY DIFFRACTIONr_angle_other_deg1.1841.5744134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.525241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24324.64384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68315339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.718157
X-RAY DIFFRACTIONr_chiral_restr0.0530.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02341
LS refinement shellResolution: 2.34→2.4 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 30 -
Rwork0.26 677 -
all-707 -
obs--91.23 %
Refinement TLS params.Method: refined / Origin x: 18.393 Å / Origin y: 26.573 Å / Origin z: -0.241 Å
111213212223313233
T0.0132 Å20.0084 Å20.0129 Å2-0.1655 Å20.0356 Å2--0.5966 Å2
L1.4774 °20.305 °20.2502 °2-4.724 °20.5199 °2--0.8708 °2
S0.118 Å °0.033 Å °0.027 Å °-0.0927 Å °0.0113 Å °0.2849 Å °-0.0117 Å °-0.1054 Å °-0.1293 Å °

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