[English] 日本語
Yorodumi
- PDB-1rxz: C-terminal region of A. fulgidus FEN-1 complexed with A. fulgidus PCNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rxz
TitleC-terminal region of A. fulgidus FEN-1 complexed with A. fulgidus PCNA
Components
  • DNA polymerase sliding clampDNA clamp
  • Flap structure-specific endonuclease
KeywordsREPLICATION / beta-zipper / interdomain connecting loop / DNA repair / DNA replication
Function / homology
Function and homology information


5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding / DNA 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 / 5'-3' exonuclease / 5'-3' exonuclease / 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 / Flap endonuclease 1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChapados, B.R. / Hosfield, D.J. / Han, S. / Qiu, J. / Yelent, B. / Shen, B. / Tainer, J.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structural Basis for FEN-1 Substrate Specificity and PCNA-Mediated Activation in DNA Replication and Repair
Authors: Chapados, B.R. / Hosfield, D.J. / Han, S. / Qiu, J. / Yelent, B. / Shen, B. / Tainer, J.A.
History
DepositionDec 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase sliding clamp
B: Flap structure-specific endonuclease


Theoretical massNumber of molelcules
Total (without water)28,6702
Polymers28,6702
Non-polymers00
Water1,60389
1
A: DNA polymerase sliding clamp
B: Flap structure-specific endonuclease

A: DNA polymerase sliding clamp
B: Flap structure-specific endonuclease

A: DNA polymerase sliding clamp
B: Flap structure-specific endonuclease


Theoretical massNumber of molelcules
Total (without water)86,0106
Polymers86,0106
Non-polymers00
Water1086
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)86.530, 86.530, 96.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-541-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by applying the following transformations: ROTATION: [-0.5 -0.86603 0] [0.86603 -0.5 0] [0 0 1] TRANSLATION: 86.53304 -0.00002 0.00002 AND ROTATION: [-0.5 0.86603 0] [-0.86603 -0.5 0] [0 0 1] TRANSLATION: 43.26651 74.9398 0.00003

-
Components

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


Mass: 27301.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: PCN, AF0335 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29912
#2: Protein/peptide Flap structure-specific endonuclease


Mass: 1368.536 Da / Num. of mol.: 1 / Fragment: PCNA-binding motif / Source method: obtained synthetically
Details: synthetic peptide derived from the PCNA-binding motif of afFEN-1
References: UniProt: O29975
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Na/K phosphate, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
250 mMTris1droppH8.0
3250 mM1dropNaCl
41.4-1.6 Msodium/pootassium phosphate1reservoirpH9.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2003
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. all: 36466 / Num. obs: 36466 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.08
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.457 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RWZ

1rwz


Resolution: 2→60 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Carried out twinned refinement in CNS, against the least squares residual for hemihedral twinning. The twinning operator is: h,-h-k,-l. The twin fraction is: 0.370
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3472 -randomly selected in the shells to ensure that twin-related reflections were selected in pairs
Rwork0.18 ---
all0.189 36330 --
obs0.189 36330 99.4 %-
Refinement stepCycle: LAST / Resolution: 2→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 0 89 2102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.29
X-RAY DIFFRACTIONx_torsion_deg25.3
X-RAY DIFFRACTIONx_torsion_impr_deg0.74
Refinement
*PLUS
Rfactor Rfree: 0.26 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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