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Yorodumi- PDB-2v79: Crystal Structure of the N-terminal domain of DnaD from Bacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v79 | ||||||
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Title | Crystal Structure of the N-terminal domain of DnaD from Bacillus Subtilis | ||||||
Components | DNA REPLICATION PROTEIN DNAD | ||||||
Keywords | DNA BINDING PROTEIN / PRIMOSOME / DNA-BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2 Å | ||||||
Authors | Schneider, S. / Zhang, W. / Soultanas, P. / Paoli, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structure of the N-Terminal Oligomerization Domain of Dnad Reveals a Unique Tetramerization Motif and Provides Insights Into Scaffold Formation. Authors: Schneider, S. / Zhang, W. / Soultanas, P. / Paoli, M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Crystallization and X-Ray Diffraction Analysis of the DNA-Remodelling Protein Dnad from Bacillus Subtilis Authors: Schneider, S. / Carneiro, M.J.V.M. / Charikleia, I. / Soultanas, P. / Paoli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v79.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v79.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 2v79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v79_validation.pdf.gz | 438.7 KB | Display | wwPDB validaton report |
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Full document | 2v79_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 2v79_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 2v79_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/2v79 ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v79 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.8548, -0.09045, -0.511), Vector: |
-Components
#1: Protein | Mass: 16079.396 Da / Num. of mol.: 2 / Fragment: N-TERMINAL OLIGOMERIZATION DOMAIN, RESIDUES 1-127 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 EMG50 / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3), B834 (DE3) / References: UniProt: P39787 #2: Chemical | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Sequence details | THE N-TERMINAL DOMAIN INCLUDES RESIDUES 1-128 WITH AN ADDITIONAL | |
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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: 3.3 Å3/Da / Density % sol: 62.9 % / Description: NONE |
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Crystal grow | Details: 0.1M SODIUMACETATE, 3.2M SODIUMCHLORIDE |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE-PLATE / Detector: IMAGE PLATE / Date: May 27, 2006 / Details: VARIMAX HF OPTICS |
Radiation | Monochromator: NI FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→28 Å / Num. obs: 30662 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.638 / SU ML: 0.074 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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