[English] 日本語
Yorodumi
- PDB-1isq: Pyrococcus furiosus PCNA complexed with RFCL PIP-box peptide -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of DNA replication / DNA replication / DNA binding / ATP binding
Similarity search - Function
Replication factor C, large subunit / 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 ...Replication factor C, large subunit / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.66 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

-
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

-
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

+
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