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Yorodumi- PDB-3gxv: Three-dimensional structure of N-terminal domain of DnaB Helicase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gxv | ||||||
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Title | Three-dimensional structure of N-terminal domain of DnaB Helicase from Helicobacter pylori and its interactions with primase | ||||||
Components | (Replicative DNA helicase) x 3 | ||||||
Keywords | HYDROLASE/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 DNA 5'-3' helicase / primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / 5'-3' DNA helicase activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kashav, T. / Nitharwal, R. / Syed, A.A. / Gabdoulkhakov, A. / Saenger, W. / Dhar, K.S. / Gourinath, S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gxv.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gxv.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/3gxv ftp://data.pdbj.org/pub/pdb/validation_reports/gx/3gxv | HTTPS FTP |
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-Related structure data
Related structure data | 2r5uS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 | | 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 | | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.45 Å3/Da / Density % sol: 72.37 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.997 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.3451 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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