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Yorodumi- PDB-3hdt: Crystal structure of putative kinase from Clostridium symbiosum A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hdt | ||||||
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Title | Crystal structure of putative kinase from Clostridium symbiosum ATCC 14940 | ||||||
Components | putative kinase | ||||||
Keywords | structural genomics / unknown function / Clostridium symbiosum ATCC 14940 / putative kinase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION Function and homology information | ||||||
Biological species | Clostridium symbiosum ATCC 14940 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.79 Å | ||||||
Authors | Chang, C. / Freeman, L. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of putative kinase from Clostridium symbiosum ATCC 14940 Authors: Chang, C. / Freeman, L. / Jedrzejczak, R. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hdt.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hdt.ent.gz | 62.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/3hdt ftp://data.pdbj.org/pub/pdb/validation_reports/hd/3hdt | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | dimer as is |
-Components
#1: Protein | Mass: 26113.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium symbiosum ATCC 14940 (bacteria) Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)magic #2: Chemical | #3: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.42 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M Acetic Acid pH 4.5, 20% 1,4-butanediol, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2008 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→50 Å / Num. all: 13107 / Num. obs: 13096 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.9 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 44 |
Reflection shell | Resolution: 2.8→2.82 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 5 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.79→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 30.613 / SU ML: 0.285 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.859 / ESU R Free: 0.37 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.172 Å2
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Refinement step | Cycle: LAST / Resolution: 2.79→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.79→2.863 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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