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- PDB-3ec2: Crystal structure of the DnaC helicase loader -

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Basic information

Entry
Database: PDB / ID: 3ec2
TitleCrystal structure of the DnaC helicase loader
ComponentsDNA replication protein DnaC
KeywordsREPLICATION / helicase loader / replication initiation factor / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


DNA replication / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
IstB-like ATP-binding protein / IstB-like ATP binding protein / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA replication protein DnaC
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsMott, M.L. / Erzberger, J.P. / Coons, M.M. / Berger, J.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators.
Authors: Mott, M.L. / Erzberger, J.P. / Coons, M.M. / Berger, J.M.
History
DepositionAug 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA replication protein DnaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2643
Polymers20,8131
Non-polymers4522
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.492, 84.492, 51.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein DNA replication protein DnaC


Mass: 20812.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: dnaC, aq_910 / Production host: Escherichia coli (E. coli) / References: UniProt: O67056
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM Tris, 1% PEG 6K, 1mM TCEP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9795, 1.11587
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 16, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.115871
ReflectionResolution: 2.25→50 Å / Num. obs: 5534 / Biso Wilson estimate: 39.424 Å2 / Rsym value: 0.05

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ELVESrefinement
SOLVEphasing
RefinementResolution: 2.7→50 Å / WRfactor Rfree: 0.282 / WRfactor Rwork: 0.221 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.761 / SU Rfree: 0.408 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 265 -random
Rwork0.233 ---
all-5534 --
obs-5534 100 %-
Displacement parametersBiso max: 111.26 Å2 / Biso mean: 67.597 Å2 / Biso min: 21.88 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 28 47 1509
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.019
X-RAY DIFFRACTIONr_angle_refined_deg1.985

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