[English] 日本語
Yorodumi
- PDB-5dai: Proliferating cell nuclear antigen homolog 1 bound to FEN-1 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dai
TitleProliferating cell nuclear antigen homolog 1 bound to FEN-1 peptide
Components
  • C-terminus of FEN-1 protein
  • DNA polymerase sliding clamp 1DNA clamp
KeywordsTRANSFERASE / complex / PIP box binder
Function / homology
Function and homology information


5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / leading strand elongation / DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding ...5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / leading strand elongation / DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding / DNA binding / identical protein binding
Similarity search - Function
Flap structure-specific endonuclease, archaea / Flap endonuclease 1 / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...Flap structure-specific endonuclease, archaea / Flap endonuclease 1 / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / 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 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / : / PIN-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
DNA polymerase sliding clamp 1 / Flap endonuclease 1
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
Thermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLadner, J.E. / Altieri, A.S. / Kelman, Z.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp.
Authors: Altieri, A.S. / Ladner, J.E. / Li, Z. / Robinson, H. / Sallman, Z.F. / Marino, J.P. / Kelman, Z.
History
DepositionAug 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase sliding clamp 1
B: C-terminus of FEN-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,56713
Polymers30,5102
Non-polymers1,05711
Water1,76598
1
A: DNA polymerase sliding clamp 1
B: C-terminus of FEN-1 protein
hetero molecules

A: DNA polymerase sliding clamp 1
B: C-terminus of FEN-1 protein
hetero molecules

A: DNA polymerase sliding clamp 1
B: C-terminus of FEN-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,70039
Polymers91,5306
Non-polymers3,17033
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13350 Å2
ΔGint-419 kcal/mol
Surface area33590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.070, 152.070, 35.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

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


Mass: 29099.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: pcn1, TK0535 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JF32
#2: Protein/peptide C-terminus of FEN-1 protein


Mass: 1410.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermococcus kodakarensis KOD1 (archaea) / References: UniProt: Q5JGN0*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: Well solution: 2.8 M ammonium sulfate, 100 mM citric acid buffer pH 5.3, and 10% PEG 4000.
Temp details: room temperature

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→28.8 Å / Num. obs: 20143 / % possible obs: 98.2 % / Redundancy: 3.31 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LX1

3lx1


Resolution: 2→28.762 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 1025 5.09 %random
Rwork0.1815 ---
obs0.1835 20133 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 55 98 2202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082198
X-RAY DIFFRACTIONf_angle_d1.1362969
X-RAY DIFFRACTIONf_dihedral_angle_d14.834842
X-RAY DIFFRACTIONf_chiral_restr0.046329
X-RAY DIFFRACTIONf_plane_restr0.004379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.10560.33071520.27352770X-RAY DIFFRACTION100
2.1056-2.23750.3221480.23472753X-RAY DIFFRACTION100
2.2375-2.41010.31671430.23432783X-RAY DIFFRACTION99
2.4101-2.65250.31461490.22812733X-RAY DIFFRACTION99
2.6525-3.0360.32171620.21442738X-RAY DIFFRACTION98
3.036-3.82360.19281490.16592701X-RAY DIFFRACTION97
3.8236-28.76470.15751220.14992630X-RAY DIFFRACTION94

+
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