+Open data
-Basic information
Entry | Database: PDB / ID: 2dvp | ||||||
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Title | Structure of NTPase from Pyroccous horikoshii | ||||||
Components | Hypothetical protein PH1917 | ||||||
Keywords | HYDROLASE / NTPase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information XTP/dITP diphosphatase / purine nucleoside triphosphate catabolic process / ITP diphosphatase activity / XTP diphosphatase activity / dITP diphosphatase activity / nucleotide metabolic process / ribonucleoside triphosphate phosphatase activity / nucleotide binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Lokanath, N.K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structures of dimeric nonstandard nucleotide triphosphate pyrophosphatase from Pyrococcus horikoshii OT3: functional significance of interprotomer conformational changes Authors: Lokanath, N.K. / Pampa, K.J. / Takio, K. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dvp.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dvp.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dvp_validation.pdf.gz | 421.5 KB | Display | wwPDB validaton report |
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Full document | 2dvp_full_validation.pdf.gz | 423.6 KB | Display | |
Data in XML | 2dvp_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 2dvp_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/2dvp ftp://data.pdbj.org/pub/pdb/validation_reports/dv/2dvp | HTTPS FTP |
-Related structure data
Related structure data | 1v7rSC 2dvnC 2dvoC 2ztiC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21233.420 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (DE3)-RIL / References: UniProt: O59580 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.83 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 4.6 Details: NaCl, acetate, pH 4.6, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 28, 2004 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 17606 / Num. obs: 16658 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V7R Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.199 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 32.5052 Å / Origin y: 41.6165 Å / Origin z: 39.0135 Å
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