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- PDB-3gxv: Three-dimensional structure of N-terminal domain of DnaB Helicase... -

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Basic information

Entry
Database: PDB / ID: 3gxv
TitleThree-dimensional structure of N-terminal domain of DnaB Helicase from Helicobacter pylori and its interactions with primase
Components(Replicative DNA helicase) x 3
KeywordsHYDROLASE/REPLICATION / Hexameric helicase / Helicobacter pylori / primase / replication / ATP-binding / Autocatalytic cleavage / DNA replication / DNA-binding Hydrolase / Nucleotide-binding / Primosome / DNA-binding / Helicase / Hydrolase / HYDROLASE-REPLICATION COMPLEX
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. ...DNAb Helicase; Chain A / DNAb Helicase; Chain A / DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Replicative DNA helicase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKashav, T. / Nitharwal, R. / Syed, A.A. / Gabdoulkhakov, A. / Saenger, W. / Dhar, K.S. / Gourinath, S.
CitationJournal: Plos One / Year: 2009
Title: Three-dimensional structure of N-terminal domain of DnaB helicase and helicase-primase interactions in Helicobacter pylori
Authors: Kashav, T. / Nitharwal, R. / Abdulrehman, S.A. / Gabdoulkhakov, A. / Saenger, W. / Dhar, S.K. / Gourinath, S.
History
DepositionApr 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replicative DNA helicase
B: Replicative DNA helicase
C: Replicative DNA helicase
D: Replicative DNA helicase


Theoretical massNumber of molelcules
Total (without water)34,0494
Polymers34,0494
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replicative DNA helicase

A: Replicative DNA helicase
C: Replicative DNA helicase
D: Replicative DNA helicase


Theoretical massNumber of molelcules
Total (without water)34,0494
Polymers34,0494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-32 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.830, 78.150, 108.000
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 Replicative DNA helicase


Mass: 14291.337 Da / Num. of mol.: 2 / Fragment: N-terminal domain, residues 1-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1362 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O25916, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein/peptide Replicative DNA helicase


Mass: 2489.978 Da / Num. of mol.: 1 / Fragment: residues 101-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1362 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O25916, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Protein/peptide Replicative DNA helicase


Mass: 2976.450 Da / Num. of mol.: 1 / Fragment: residues 98-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1362 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O25916, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 4.45 Å3/Da / Density % sol: 72.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Bis Tris, Ammonium Sulphate, Sodium malonate, Peg 550MME, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.997 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.2→19.32 Å / Num. obs: 30563 / Redundancy: 5.32 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.095 / Net I/σ(I): 9.78
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.35 / Num. unique all: 6637 / Rsym value: 0.575

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2r5u

2r5u


Resolution: 2.2→19.32 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 52275.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.278 3981 6.9 %RANDOM
Rwork0.249 ---
obs0.249 30561 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.3451 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 0 0 195 2582
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 631 6.9 %
Rwork0.285 8537 -
obs--92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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