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- PDB-2w58: Crystal Structure of the DnaI -

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Basic information

Entry
Database: PDB / ID: 2w58
TitleCrystal Structure of the DnaI
ComponentsPRIMOSOME COMPONENT (HELICASE LOADER)
KeywordsHYDROLASE / DNAI / HELICASE / ATP-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


helicase activity / ATP binding
Similarity search - Function
Primosomal DnaI, N-terminal / Primosomal protein DnaI N-terminus / 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 / PHOSPHATE ION / Primosome component (Helicase loader)
Similarity search - Component
Biological speciesGEOBACILLUS KAUSTOPHILUS HTA426 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTsai, K.L. / Lo, Y.H. / Sun, Y.J. / Hsiao, C.D.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Molecular Interplay between the Replicative Helicase Dnac and its Loader Protein Dnai from Geobacillus Kaustophilus.
Authors: Tsai, K.L. / Lo, Y.H. / Sun, Y.J. / Hsiao, C.D.
History
DepositionDec 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary / Version format compliance
Revision 1.2Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRIMOSOME COMPONENT (HELICASE LOADER)
B: PRIMOSOME COMPONENT (HELICASE LOADER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6695
Polymers47,1222
Non-polymers5463
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-6.7 kcal/mol
Surface area22480 Å2
MethodPQS
Unit cell
Length a, b, c (Å)54.632, 59.530, 115.636
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 PRIMOSOME COMPONENT (HELICASE LOADER) / / DNAI


Mass: 23561.158 Da / Num. of mol.: 2 / Fragment: RESIDUES 108-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS KAUSTOPHILUS HTA426 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5KWD0
#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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.07 Å3/Da / Density % sol: 39.97 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: reservoir solution 100 mM Hepes (pH 7.2), 50 mM MgCl2, 20% PEG polyethylene glycol) 3550 and 50 mM Na2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 13546 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 26
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.2refinement
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.77 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 24788.16 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: BULK SOLVENT MODEL USED THE RESIDUES IN CHAIN A INCLUDING 108-110, 208-210, 235- 237 AND 279-283 WERE MISSING. THE RESIDUES IN CHAIN B INCLUDING 108-111, 277- 280 AND 305-309 WERE MISSING.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 925 8.1 %RANDOM
Rwork0.235 ---
obs0.235 11410 83.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.27 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 63.1 Å2
Baniso -1Baniso -2Baniso -3
1-20.22 Å20 Å20 Å2
2---11.93 Å20 Å2
3----8.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 33 166 3276
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.571.5
X-RAY DIFFRACTIONc_mcangle_it5.572
X-RAY DIFFRACTIONc_scbond_it5.222
X-RAY DIFFRACTIONc_scangle_it7.092.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
Rfactor% reflection
Rfree0.302 8.7 %
Rwork0.274 -
obs-60.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ADP.PARAMADP.TOP

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