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Yorodumi- PDB-1b78: STRUCTURE-BASED IDENTIFICATION OF THE BIOCHEMICAL FUNCTION OF A H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b78 | ||||||
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Title | STRUCTURE-BASED IDENTIFICATION OF THE BIOCHEMICAL FUNCTION OF A HYPOTHETICAL PROTEIN FROM METHANOCOCCUS JANNASCHII:MJ0226 | ||||||
Components | PYROPHOSPHATASE | ||||||
Keywords | STRUCTURAL GENOMICS / PYROPHOSPHATASE / HYPERTHERMAL PROTEIN | ||||||
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 / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.2 Å | ||||||
Authors | Hwang, K.Y. / Chung, J.H. / Han, Y.S. / Kim, S.H. / Cho, Y. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Structure-based identification of a novel NTPase from Methanococcus jannaschii. Authors: Hwang, K.Y. / Chung, J.H. / Kim, S.H. / Han, Y.S. / Cho, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b78.cif.gz | 89.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b78.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 1b78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/1b78 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/1b78 | HTTPS FTP |
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-Related 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: 22232.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methanocaldococcus jannaschii (archaea) / References: UniProt: Q57679 #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: 2.57 Å3/Da / Density % sol: 52.12 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Wavelength: 1.542 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 23663 / % possible obs: 95 % / Redundancy: 5.3 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 5.5 |
-Processing
Software | Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MIR / Resolution: 2.2→6 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 22.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.33 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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