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- PDB-2chv: Replication Factor C ADPNP complex -

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Basic information

Entry
Database: PDB / ID: 2chv
TitleReplication Factor C ADPNP complex
ComponentsREPLICATION FACTOR C SMALL SUBUNIT
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / DNA REPLICATION / CLAMP LOADER / AAA+ ATPASE / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


Rad17 RFC-like complex / DNA replication factor C complex / Elg1 RFC-like complex / DNA clamp loader activity / DNA-templated DNA replication / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Replication factor C small subunit, archaeal / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Replication factor C, C-terminal / Replication factor C C-terminal domain / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) ...Replication factor C small subunit, archaeal / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Replication factor C, C-terminal / Replication factor C C-terminal domain / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Replication factor C small subunit
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 4 Å
AuthorsSeybert, A. / Singleton, M.R. / Cook, N. / Hall, D.R. / Wigley, D.B.
CitationJournal: Embo J. / Year: 2006
Title: Communication between Subunits within an Archaeal Clamp-Loader Complex.
Authors: Seybert, A. / Singleton, M.R. / Cook, N. / Hall, D.R. / Wigley, D.B.
History
DepositionMar 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: REPLICATION FACTOR C SMALL SUBUNIT
B: REPLICATION FACTOR C SMALL SUBUNIT
C: REPLICATION FACTOR C SMALL SUBUNIT
D: REPLICATION FACTOR C SMALL SUBUNIT
E: REPLICATION FACTOR C SMALL SUBUNIT
F: REPLICATION FACTOR C SMALL SUBUNIT


Theoretical massNumber of molelcules
Total (without water)216,2376
Polymers216,2376
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)123.907, 134.225, 146.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
REPLICATION FACTOR C SMALL SUBUNIT / REPLICATION FACTOR C / RFC SMALL SUBUNIT / CLAMP LOADER SMALL SUBUNIT / AFRFC SMALL SUBUNIT / AFRFCSM


Mass: 36039.562 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O28219

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.31 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 4→20 Å / Num. obs: 20931 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.09

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Processing

RefinementMethod to determine structure: OTHER / Resolution: 4→20 Å
Details: THIS STRUCTURE IS A RIGID BODY FIT OF THE INDIVIDUAL DOMAINS OF THE RFC SMALL SUBUNIT AGAINST THE DATA AND HAS NOT BEEN REFINED FURTHER
RfactorNum. reflection% reflectionSelection details
Rfree0.4984 1045 4.9 %RANDOM
Rwork0.4917 ---
obs-20138 --
Refinement stepCycle: LAST / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14838 0 0 0 14838

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