[English] 日本語
Yorodumi
- PDB-7o1e: Crystal structure of PCNA from Chaetomium thermophilum -

+
Open data


ID or keywords:

Loading...

-
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


DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / DNA repair / DNA binding / nucleus
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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 °

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more