[English] 日本語
Yorodumi
- PDB-1fgu: SSDNA-BINDING DOMAIN OF THE LARGE SUBUNIT OF REPLICATION PROTEIN A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fgu
TitleSSDNA-BINDING DOMAIN OF THE LARGE SUBUNIT OF REPLICATION PROTEIN A
ComponentsREPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT
KeywordsREPLICATION / OB-fold / ssDNA-binding protein
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / single-stranded telomeric DNA binding / chromatin-protein adaptor activity / G-rich strand telomeric DNA binding / protein localization to site of double-strand break / Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...protein localization to chromosome / DNA replication factor A complex / single-stranded telomeric DNA binding / chromatin-protein adaptor activity / G-rich strand telomeric DNA binding / protein localization to site of double-strand break / Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / HSF1 activation / telomere maintenance via telomerase / mismatch repair / SUMOylation of DNA damage response and repair proteins / Activation of ATR in response to replication stress / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / G2/M DNA damage checkpoint / base-excision repair / PML body / Meiotic recombination / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / site of double-strand break / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / chromosome, telomeric region / DNA replication / DNA repair / DNA damage response / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain ...Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Replication protein A 70 kDa DNA-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsBochkareva, E. / Belegu, V. / Korolev, S. / Bochkarev, A.
Citation
Journal: EMBO J. / Year: 2001
Title: Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding.
Authors: Bochkareva, E. / Belegu, V. / Korolev, S. / Bochkarev, A.
#1: Journal: Nature / Year: 1997
Title: Structure of the Single-stranded-DNA-binding Domain of Replication Protein A Bound to DNA
Authors: Bochkarev, A. / Pfuetzner, R.A. / Edwards, A.M. / Frappier, L.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: Replication Protein A: Characterization and Crystallization of the DNA-binding Domain
Authors: Pfuetzner, R.A. / Bochkarev, A. / Frappier, L. / Edwards, A.M.
History
DepositionJul 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT
B: REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT


Theoretical massNumber of molelcules
Total (without water)56,2192
Polymers56,2192
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.500, 84.860, 119.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a trimer of 70, 32, and 14 kDa subunit THE BIOLOGICAL ASSEMBLY IS A TRIMER OF 70, 32, and 14 KDA SUBUNITS

-
Components

#1: Protein REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT / SINGLE-STRANDED DNA-BINDING PROTEIN / REPLICATION FACTOR-A PROTEIN 1 / RF-A / RP-A


Mass: 28109.641 Da / Num. of mol.: 2 / Fragment: CENTRAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid details: BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P27694
#2: Water ChemComp-HOH / 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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M K,NaH2PO4 0.1 M Tris 3.8 M NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18-10 mg/mlprotein1drop
215 mMHEPES1drop
3350 mM1dropNaCl
45 mMdithiothreitol1drop
50.1 Msodium potassium phospahte1reservoir
60.1 MTris1reservoir
73.8 M1reservoirNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033
DetectorType: SBC-2 / Detector: CCD / Date: Jan 27, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 247836 / Num. obs: 22963 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 57.6 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 37.1
Reflection shellResolution: 2.49→2.58 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.6 / Num. unique all: 2191 / % possible all: 96
Reflection
*PLUS
Num. measured all: 247836
Reflection shell
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.19

-
Processing

Software
NameVersionClassification
PHASESphasing
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / σ(F): 1.5 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: CRYSTALS DIFFRACTED ANYSOTROPICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1771 10 %RANDOM
Rwork0.215 ---
obs0.215 19729 86.2 %-
all-22875 --
Solvent computationSolvent model: CNS DEFAULT BULK SOLVENT / Bsol: 39.1 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 56.99 Å2
Baniso -1Baniso -2Baniso -3
1--14.4 Å20 Å20 Å2
2---3.8 Å20 Å2
3---18.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 0 32 3827
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_torsion_deg25.8
X-RAY DIFFRACTIONc_torsion_impr_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.75
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.32.5
X-RAY DIFFRACTIONc_mcangle_it33
X-RAY DIFFRACTIONc_scbond_it3.63
X-RAY DIFFRACTIONc_scangle_it4.33.5
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 10
Num. reflection% reflection
Rfree99 4.4 %
Rwork1360 -
obs-64.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.75
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
X-RAY DIFFRACTIONc_mcbond_it2.32.5
X-RAY DIFFRACTIONc_scbond_it3.63
X-RAY DIFFRACTIONc_mcangle_it33
X-RAY DIFFRACTIONc_scangle_it4.33.5
LS refinement shell
*PLUS
% reflection Rfree: 4.4 %

+
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