+Open data
-Basic information
Entry | Database: PDB / ID: 1b79 | ||||||
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Title | N-TERMINAL DOMAIN OF DNA REPLICATION PROTEIN DNAB | ||||||
Components | DnaB Helicase | ||||||
Keywords | HYDROLASE / HELICASE / HEXAMER / DNA REPLICATION | ||||||
Function / homology | Function and homology information DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / DNA helicase complex / DNA 5'-3' helicase / primosome complex / DNA replication, synthesis of primer / replisome ...DnaB-DnaC complex / DnaB-DnaC-Rep-PriC complex / DnaB-DnaG complex / DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / DNA helicase complex / DNA 5'-3' helicase / primosome complex / DNA replication, synthesis of primer / replisome / DNA duplex unwinding / response to ionizing radiation / DNA unwinding involved in DNA replication / replication fork processing / DNA replication initiation / DNA helicase activity / helicase activity / 5'-3' DNA helicase activity / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å | ||||||
Authors | Fass, D. / Bogden, C.E. / Berger, J.M. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Crystal structure of the N-terminal domain of the DnaB hexameric helicase. Authors: Fass, D. / Bogden, C.E. / Berger, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b79.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b79.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 1b79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/1b79 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/1b79 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 13222.717 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Details: hexamers not associated in crystal / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PLYSS References: UniProt: P0ACB0, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #2: 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: 2.36 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.9 / Details: pH 6.9, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | Name: SODIUM CACODYLATE | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 118 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9667 |
Detector | Date: Feb 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9667 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 21651 / % possible obs: 98.7 % / Redundancy: 3.4 % / Rsym value: 6.9 / Net I/σ(I): 9 |
Reflection | *PLUS Rmerge(I) obs: 0.069 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.008 / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 8 /
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