[English] 日本語
Yorodumi
- PDB-7n5k: PCNA from Thermococcus gammatolerans: crystal II, collection 1, 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n5k
TitlePCNA from Thermococcus gammatolerans: crystal II, collection 1, 1.98 A, 3.84 MGy
ComponentsDNA polymerase sliding clamp
KeywordsDNA BINDING PROTEIN / PCNA / sliding clamp / radioresistance / radiation damage / ionizing radiation
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
Similarity search - Component
Biological speciesThermococcus gammatolerans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsMarin-Tovar, Y. / Rudino-Pinera, E.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN209920 Mexico
CitationJournal: Proteins / Year: 2022
Title: PCNA from Thermococcus gammatolerans: A protein involved in chromosomal DNA metabolism intrinsically resistant at high levels of ionizing radiation.
Authors: Marin-Tovar, Y. / Serrano-Posada, H. / Diaz-Vilchis, A. / Rudino-Pinera, E.
History
DepositionJun 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 2023Group: 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: DNA polymerase sliding clamp
B: DNA polymerase sliding clamp
C: DNA polymerase sliding clamp
D: DNA polymerase sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,15340
Polymers120,7664
Non-polymers3,38736
Water5,765320
1
A: DNA polymerase sliding clamp
B: DNA polymerase sliding clamp
hetero molecules

C: DNA polymerase sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,11730
Polymers90,5753
Non-polymers2,54227
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/21
Buried area10050 Å2
ΔGint-214 kcal/mol
Surface area32170 Å2
MethodPISA
2
D: DNA polymerase sliding clamp
hetero molecules

D: DNA polymerase sliding clamp
hetero molecules

D: DNA polymerase sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,10930
Polymers90,5753
Non-polymers2,53427
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area10040 Å2
ΔGint-191 kcal/mol
Surface area32460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.920, 186.920, 64.031
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

-
Components

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


Mass: 30191.521 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3) (archaea)
Strain: DSM 15229 / JCM 11827 / EJ3 / Gene: pcn, TGAM_1046 / Plasmid: pCold-I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5A5N6
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.2
Details: 100 mM sodium citrate pH 5.2, 3.2 M ammonium sulfate, 7.5% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→32.125 Å / Num. obs: 89151 / % possible obs: 99.89 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.2237 / Net I/σ(I): 24.34
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.004 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 8861 / CC1/2: 0.828 / % possible all: 99.86

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A6D

5a6d


Resolution: 1.98→32.125 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 4399 4.94 %
Rwork0.1898 84686 -
obs0.1917 89085 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.02 Å2 / Biso mean: 47.5391 Å2 / Biso min: 25 Å2
Refinement stepCycle: final / Resolution: 1.98→32.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7848 0 198 320 8366
Biso mean--73.78 50.7 -
Num. residues----990
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9801-2.00250.31321620.26412828100
2.0025-2.02610.28771290.26062801100
2.0261-2.05080.29731170.26072813100
2.0508-2.07680.30341500.24872842100
2.0768-2.10410.2671690.24082756100
2.1041-2.13290.28341530.23662789100
2.1329-2.16340.27761470.23142791100
2.1634-2.19570.27161520.22392848100
2.1957-2.230.25171140.22382804100
2.23-2.26650.27681570.21152806100
2.2665-2.30560.27931800.22482755100
2.3056-2.34750.23711380.20382824100
2.3475-2.39260.23231320.20572832100
2.3926-2.44140.26141650.20712792100
2.4414-2.49450.2631290.2142834100
2.4945-2.55250.30231570.22082805100
2.5525-2.61630.26951320.21472801100
2.6163-2.6870.24231240.20752857100
2.687-2.76610.27331380.19382834100
2.7661-2.85530.24191660.19682786100
2.8553-2.95730.22831640.19132803100
2.9573-3.07560.23431570.19632836100
3.0756-3.21540.23471710.19382805100
3.2154-3.38480.23011250.17882861100
3.3848-3.59660.22471440.16752840100
3.5966-3.87390.21751190.17062855100
3.8739-4.26290.19611400.16682870100
4.2629-4.87790.16921610.14962806100
4.8779-6.13860.21731550.18292870100
6.1386-32.1250.2041520.2025294299

+
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