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- PDB-3ecc: Crystal structure of the DnaC helicase loader in complex with ADP-BeF3 -

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Basic information

Entry
Database: PDB / ID: 3ecc
TitleCrystal structure of the DnaC helicase loader in complex with ADP-BeF3
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA replication protein DnaC
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMott, M.L. / Erzberger, J.P. / Coons, M.M. / Berger, J.
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 29, 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 / Item: _software.classification
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: DNA replication protein DnaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7664
Polymers21,2481
Non-polymers5183
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.582, 84.582, 49.587
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: 21248.309 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 / Adenosine 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: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 294 K / pH: 8
Details: 50mM Tris, 1% PEG 6000, 1mM TCEP, 2mM ADP, 5mM MgCl2, 4mM BeCl2, 12mM NaF, 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: 1.11588
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 2.12→73 Å / Num. obs: 5408 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rsym value: 5.7 / Net I/σ(I): 11.6
Reflection shellResolution: 2.12→2.23 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.597

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Processing

Software
NameClassification
ELVESrefinement
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å
RfactorNum. reflectionSelection details
Rfree0.294 259 RANDOM
Rwork0.263 --
obs0.263 5408 -
all-5408 -
Displacement parametersBiso mean: 57.47 Å2
Baniso -1Baniso -2Baniso -3
1--5.13 Å2-2.56 Å20 Å2
2---5.13 Å20 Å2
3---7.69 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1471 0 32 45 1548

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