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- PDB-1iqp: Crystal Structure of the Clamp Loader Small Subunit from Pyrococc... -

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Basic information

Entry
Database: PDB / ID: 1iqp
TitleCrystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus
ComponentsRFCS
KeywordsREPLICATION / CLAMP LOADER / EXTENDED AAA-ATPASE DOMAIN / COMPLEX WITH ADP
Function / homology
Function and homology information


DNA replication factor C complex / DNA clamp loader activity / intein-mediated protein splicing / DNA-templated DNA replication / endonuclease activity / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / LAGLIDADG-like domain / Intein splicing domain / Intein / Replication factor C, C-terminal / Replication factor C C-terminal domain / : / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. ...Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / LAGLIDADG-like domain / Intein splicing domain / Intein / Replication factor C, C-terminal / Replication factor C C-terminal domain / : / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Homing endonuclease / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / 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 / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Replication factor C small subunit
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsOyama, T. / Ishino, Y. / Cann, I.K.O. / Ishino, S. / Morikawa, K.
Citation
Journal: Mol.Cell / Year: 2001
Title: Atomic Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus
Authors: Oyama, T. / Ishino, Y. / Cann, I.K.O. / Ishino, S. / Morikawa, K.
#1: Journal: J.BACTERIOL. / Year: 2001
Title: Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus
Authors: Cann, I.K.O. / Ishino, S. / Yuasa, M. / Daiyasu, H. / Toh, H. / Ishino, Y.
#2: Journal: To be Published
Title: Three-dimensional electron microscopy of the clamp loader small subunit from Pyrococcus furiosus
Authors: Mayanagi, K. / Miyata, T. / Oyama, T. / Ishino, Y. / Morikawa, K.
History
DepositionJul 24, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RFCS
B: RFCS
C: RFCS
D: RFCS
E: RFCS
F: RFCS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,46010
Polymers224,7516
Non-polymers1,7094
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23210 Å2
ΔGint-120 kcal/mol
Surface area83360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.361, 105.608, 316.898
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
RFCS / replication factor C small subunit precursor


Mass: 37458.531 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rfcs / Plasmid: PET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U4J3
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: MPD, glycerol, sodium chloride, acetic acid, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
210 mMpotassium phosphate1drop
3450 mM1dropNaCl
46 %glycerol1drop
54 mMBES1drop
60.03 mM1dropCaCl2
7100 mMacetate1reservoir
842.5-47.5 %(v/v)MPD1reservoir
95-7.5 %(v/v)glycerol1reservoir
10100 mMacetate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jul 8, 1999 / Details: mirros
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→65 Å / Num. all: 80855 / Num. obs: 76556 / % possible obs: 93.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.037 / Net I/σ(I): 30
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 4.5 / Num. unique all: 6221 / % possible all: 78.7
Reflection
*PLUS
Lowest resolution: 65 Å / Num. measured all: 260398
Reflection shell
*PLUS
% possible obs: 78.7 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.8→15 Å / Isotropic thermal model: isotripic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3847 5.35 %random
Rwork0.224 ---
obs-71970 --
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15679 0 108 244 16031
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 15 Å / σ(F): 1 / % reflection Rfree: 5.35 % / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.16

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