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Yorodumi- PDB-1tf9: Streptomyces griseus aminopeptidase complexed with P-Iodo-L-Pheny... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tf9 | ||||||
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Title | Streptomyces griseus aminopeptidase complexed with P-Iodo-L-Phenylalanine | ||||||
Components | Aminopeptidase | ||||||
Keywords | HYDROLASE / DOUBLE-ZINC METALLOPROTEINASE / CALCIUM ACTIVATION / PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information aminopeptidase S / metalloexopeptidase activity / aminopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces griseus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Difference fourier from previously determined, related structure / Resolution: 1.3 Å | ||||||
Authors | Reiland, V. / Gilboa, R. / Spungin-Bialik, A. / Schomburg, D. / Shoham, Y. / Blumberg, S. / Shoham, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Binding of inhibitory aromatic amino acids to Streptomyces griseus aminopeptidase. Authors: Reiland, V. / Gilboa, R. / Spungin-Bialik, A. / Schomburg, D. / Shoham, Y. / Blumberg, S. / Shoham, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tf9.cif.gz | 135 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tf9.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/1tf9 ftp://data.pdbj.org/pub/pdb/validation_reports/tf/1tf9 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29750.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: THE ENZYME IS ISOLATED FROM THE COMMERCIALLY AVAILABLE ENZYME MIXTURE "PRONASE E" Source: (natural) Streptomyces griseus (bacteria) References: UniProt: P80561, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-PHI / | #5: 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: 2.24 Å3/Da / Density % sol: 44.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 4000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 / Wavelength: 0.9793 Å | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 27, 2001 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.3→20 Å / Num. all: 63168 / Num. obs: 63168 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Rsym value: 0.045 / Net I/σ(I): 17.2 | |||||||||
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 11 % / Rsym value: 0.162 / % possible all: 57.8 |
-Processing
Software |
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Refinement | Method to determine structure: Difference fourier from previously determined, related structure Resolution: 1.3→20 Å / Num. parameters: 23452 / Num. restraintsaints: 28850 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 23 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2505.59 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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Refine LS restraints |
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