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Yorodumi- PDB-1f89: Crystal structure of Saccharomyces cerevisiae Nit3, a member of b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f89 | ||||||
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Title | Crystal structure of Saccharomyces cerevisiae Nit3, a member of branch 10 of the nitrilase superfamily | ||||||
Components | 32.5 KDA PROTEIN YLR351C | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Nitrilase / Dimer / Four layer sandwich / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information omega-amidase / omega-amidase activity / amide catabolic process / asparagine metabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / oxaloacetate metabolic process / glutamine metabolic process / Neutrophil degranulation / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Kumaran, D. / Eswaramoorthy, S. / Studier, F.W. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proteins / Year: 2003 Title: Crystal structure of a putative CN hydrolase from yeast Authors: Kumaran, D. / Eswaramoorthy, S. / Gerchman, S.E. / Kycia, H. / Studier, F.W. / Swaminathan, S. #1: Journal: CURR.OPIN.STRUCT.BIOL. / Year: 2002 Title: Catalysis in the nitrilase superfamily. Authors: Brenner, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f89.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f89.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 1f89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/1f89 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/1f89 | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.70729, 0.019, 0.70667), Vector: Details | The biological assembly is a dimer. | |
-Components
#1: Protein | Mass: 32591.213 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P49954 #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: 2.26 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 8000, HEPES, Magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 14, 2000 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 24505 / Num. obs: 24505 / % possible obs: 81.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.096 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.429 / Num. unique all: 1062 / % possible all: 35.7 |
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT NON-CRYSTALLOGRAPHIC TWO FOLD | |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 50 Å / σ(F): 2 / Rfactor obs: 0.229 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |