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Yorodumi- PDB-3c23: Structure of a bacterial DNA damage sensor protein with non-react... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c23 | ||||||
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Title | Structure of a bacterial DNA damage sensor protein with non-reactive Ligand | ||||||
Components | DNA integrity scanning protein disA | ||||||
Keywords | DNA BINDING PROTEIN / DNA damage / DNA repair / DNA-binding | ||||||
Function / homology | Function and homology information diadenylate cyclase activity / diadenylate cyclase / : / adenylate cyclase activity / DNA repair / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Witte, G. / Hartung, S. / Buttner, K. / Hopfner, K.P. | ||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: Structural Biochemistry of a Bacterial Checkpoint Protein Reveals Diadenylate Cyclase Activity Regulated by DNA Recombination Intermediates Authors: Witte, G. / Hartung, S. / Buttner, K. / Hopfner, K.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c23.cif.gz | 154.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c23.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 3c23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/3c23 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/3c23 | HTTPS FTP |
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-Related structure data
Related structure data | 3c1ySC 3c1zC 3c21C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 42763.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9WY43 #2: Chemical | #3: 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: 2.69 Å3/Da / Density % sol: 54.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.75 Details: 0.1M MES pH 6.75, 0.17M Ammoniumacetate, 35% MPD, 1.6mM Cordycepin(3'-deoxy-ATP), VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.871 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.871 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 31941 / Num. obs: 31875 / % possible obs: 98.8 % / Redundancy: 6.65 % / Rmerge(I) obs: 0.137 / Rsym value: 0.149 / Net I/σ(I): 13.07 |
Reflection shell | Resolution: 2.51→2.66 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 5.33 / Num. unique all: 87470 / Rsym value: 0.384 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3C1Y Resolution: 2.5→50 Å / Cross valid method: random / σ(F): 0
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Solvent computation | Bsol: 38.974 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.129 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Xplor file |
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