+Open data
-Basic information
Entry | Database: PDB / ID: 3s86 | ||||||
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Title | Crystal Structure of TM0159 with bound IMP | ||||||
Components | Nucleoside-triphosphatase | ||||||
Keywords | HYDROLASE / long twisted beta strand covered by two lobes / non-canonical nucleoside triphosphatase | ||||||
Function / homology | Function and homology information XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding ...XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleoside triphosphate catabolic process / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å | ||||||
Authors | Sommerhalter, M. / Smith, C. / Awwad, K. / Desai, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural and functional characterization of a noncanonical nucleoside triphosphate pyrophosphatase from Thermotoga maritima. Authors: Awwad, K. / Desai, A. / Smith, C. / Sommerhalter, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s86.cif.gz | 165.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s86.ent.gz | 130.9 KB | Display | PDB format |
PDBx/mmJSON format | 3s86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/3s86 ftp://data.pdbj.org/pub/pdb/validation_reports/s8/3s86 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23834.539 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0159 / Plasmid: pMH1 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 References: UniProt: Q9WY06, nucleoside-triphosphate phosphatase #2: Chemical | ChemComp-IMP / #3: Chemical | ChemComp-SO4 / #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: 2.28 Å3/Da / Density % sol: 46.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: PEG3350, L-Proline, Tris-HCl pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
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Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 48209 / Num. obs: 48090 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.15→2.2 Å / Mean I/σ(I) obs: 3.05 / Num. unique all: 3160 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→28.95 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.156 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 88.39 Å2 / Biso mean: 46.8774 Å2 / Biso min: 22.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→28.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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