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Yorodumi- PDB-1huj: REFINED STRUCTURE OF YEAST INORGANIC PYROPHOSPHATASE AND ITS K61R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1huj | ||||||
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Title | REFINED STRUCTURE OF YEAST INORGANIC PYROPHOSPHATASE AND ITS K61R MUTANT | ||||||
Components | INORGANIC PYROPHOSPHATASE | ||||||
Keywords | HYDROLASE / MAGNESIUM | ||||||
Function / homology | Function and homology information Cytosolic tRNA aminoacylation / Mitochondrial tRNA aminoacylation / Pyrophosphate hydrolysis / inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Swaminathan, K. / Cooperman, B.S. / Lahti, R. / Voet, D. | ||||||
Citation | Journal: To be Published Title: Refined Structure of Yeast Inorganic Pyrophosphatase and its K61R Mutant Authors: Swaminathan, K. / Cooperman, B.S. / Lahti, R. / Voet, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1huj.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1huj.ent.gz | 100.3 KB | Display | PDB format |
PDBx/mmJSON format | 1huj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/1huj ftp://data.pdbj.org/pub/pdb/validation_reports/hu/1huj | HTTPS FTP |
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-Related structure data
Related structure data | 1hukC 1pypS S: Starting model for refinement C: citing same article (ref.) |
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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: 31809.893 Da / Num. of mol.: 2 / Mutation: K61R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P00817, inorganic diphosphatase #2: Chemical | #3: 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: 2.6 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 277 K / Method: microliter drop / pH: 6.5 Details: CRYSTALLIZATION CONDITIONS: 10 MG/ML PROTEIN IN 0.1 M MES (PH 6.5) BUFFER. 10 MICROLITER DROPS IN 9 WELL DEPRESSION PLATE IN A PLASTIC SANDWICH BOX CONTAINING 15 MILLILITER OF 0.1 M MES(PH 6. ...Details: CRYSTALLIZATION CONDITIONS: 10 MG/ML PROTEIN IN 0.1 M MES (PH 6.5) BUFFER. 10 MICROLITER DROPS IN 9 WELL DEPRESSION PLATE IN A PLASTIC SANDWICH BOX CONTAINING 15 MILLILITER OF 0.1 M MES(PH 6.5) + 16 % MPD. EVERY ALTERNATE DAY, MPD CONCENTRATION INCREASED BY 1 % UNTIL FINAL CONCENTRATION REACHED 25 %. 4 DEGREE C. WITHIN 15 DAYS, 0.2 X 0.3 X 0.4 MM CRYSTALS., microliter drops, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 26, 1995 / Details: MSC/YALE MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 31919 / % possible obs: 91.6 % / Redundancy: 2.7 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.089 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: LOW RESOLUTION STRUCTURE (PDB ENTRY 1PYP) Resolution: 2.1→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION APPLIED
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Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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