+Open data
-Basic information
Entry | Database: PDB / ID: 1xjo | ||||||
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Title | STRUCTURE OF AMINOPEPTIDASE | ||||||
Components | AMINOPEPTIDASE | ||||||
Keywords | HYDROLASE / AMINOPEPTIDASE / ZYMOGEN / ZINC | ||||||
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 / Resolution: 1.75 Å | ||||||
Authors | Greenblatt, H.M. / Barra, D. / Blumberg, S. / Shoham, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Streptomyces griseus aminopeptidase: X-ray crystallographic structure at 1.75 A resolution. Authors: Greenblatt, H.M. / Almog, O. / Maras, B. / Spungin-Bialik, A. / Barra, D. / Blumberg, S. / Shoham, G. #1: Journal: Eur.J.Biochem. / Year: 1996 Title: Aminopeptidase from S. Griseus: Primary Structure and Comparison with Other Zinc-Containing Aminopeptidases Authors: Maras, B. / Greenblatt, H.M. / Shoham, G. / Spungin-Bialik, A. / Blumberg, S. / Barra, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xjo.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xjo.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/1xjo ftp://data.pdbj.org/pub/pdb/validation_reports/xj/1xjo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 29766.656 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-PO4 / | #4: Chemical | ChemComp-CA / | #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: 2.35 Å3/Da / Density % sol: 47.57 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: 16% PEG 4K, 0.1 M SODIUM ACETATE, pH 5.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.949 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 25, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.949 Å / Relative weight: 1 |
Reflection | Num. obs: 28606 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.054 |
Reflection | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 20 Å / Num. measured all: 244396 |
-Processing
Software |
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Refinement | Resolution: 1.75→20 Å / σ(F): 0 / Stereochemistry target values: DEFAULT TNT
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Solvent computation | Solvent model: DEFAULT TNT / Bsol: 295.5 Å2 / ksol: 0.765 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.141 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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