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Yorodumi- PDB-3bg2: Crystal structure of deoxyguanosinetriphosphate triphosphohydrola... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bg2 | ||||||
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Title | Crystal structure of deoxyguanosinetriphosphate triphosphohydrolase from Flavobacterium sp. MED217 | ||||||
Components | DGTP triphosphohydrolaseDGTPase | ||||||
Keywords | HYDROLASE / Structural genomics / NYSGXRC / target 10395n / TRIPHOSPHOHYDROLASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Leeuwenhoekiella blandensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the deoxyguanosinetriphosphate triphosphohydrolase from Flavobacterium sp. MED217. Authors: Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bg2.cif.gz | 165.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bg2.ent.gz | 131.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/3bg2 ftp://data.pdbj.org/pub/pdb/validation_reports/bg/3bg2 | 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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-Components
#1: Protein | Mass: 50470.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leeuwenhoekiella blandensis (bacteria) / Strain: MED217 / Gene: MED217_16760 / Production host: Escherichia coli (E. coli) / References: UniProt: A3XHN1 #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: 3.3 Å3/Da / Density % sol: 62.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG 3000, 0.1M Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→25 Å / Num. all: 92949 / Num. obs: 92949 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.068 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.95→24.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2118287.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.8806 Å2 / ksol: 0.400099 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→24.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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