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Yorodumi- PDB-1f2p: CRYSTAL STRUCTURE OF THE STREPTOMYCES GRISEUS AMINOPEPTIDASE COMP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f2p | ||||||
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Title | CRYSTAL STRUCTURE OF THE STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH L-PHENYLALANINE | ||||||
Components | AMINOPEPTIDASE | ||||||
Keywords | HYDROLASE / AMINOPEPTIDASE / DOUBLE-ZINC METALLOPROTEINASE | ||||||
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: 1.8 Å | ||||||
Authors | Gilboa, R. / Spungin-Bialik, A. / Wohlfahrt, G. / Schomburg, D. / Blumberg, S. / Shoham, G. | ||||||
Citation | Journal: Proteins / Year: 2001 Title: Interactions of Streptomyces griseus aminopeptidase with amino acid reaction products and their implications toward a catalytic mechanism. Authors: Gilboa, R. / Spungin-Bialik, A. / Wohlfahrt, G. / Schomburg, D. / Blumberg, S. / Shoham, G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Interactions of Streptomyces griseus Aminopeptidase with a Methionine Product Analogue: a Structural Study at 1.53 A Resolution. Authors: Gilboa, R. / Greenblatt, H.M. / Perach, M. / Spungin-Bialik, A. / Lessel, U. / Wohlfahrt, G. / Schomburg, D. / Blumberg, S. / Shoham, G. #2: Journal: Eur.J.Biochem. / Year: 1998 Title: Inhibition of Streptomyces griseus Aminopeptidase and Effects of Calcium Ions on Catalysis and Binding--Comparisons with the Homologous Enzyme Aeromonas Proteolytica Aminopeptidase. Authors: Papir, G. / Spungin-Bialik, A. / Ben-Meir, D. / Fudim, E. / Gilboa, R. / Greenblatt, H.M. / Shoham, G. / Lessel, U. / Schomburg, D. / Ashkenazi, R. / Blumberg, S. #3: Journal: J.Mol.Biol. / Year: 1997 Title: Streptomyces griseus Aminopeptidase: X-ray Crystallographic Structure at 1.75A Resolution. Authors: Greenblatt, H.M. / Almog, O. / Maras, B. / Spungin-Bialik, A. / Barra, D. / 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 | 1f2p.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f2p.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 1f2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f2p_validation.pdf.gz | 373.4 KB | Display | wwPDB validaton report |
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Full document | 1f2p_full_validation.pdf.gz | 373.4 KB | Display | |
Data in XML | 1f2p_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1f2p_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/1f2p ftp://data.pdbj.org/pub/pdb/validation_reports/f2/1f2p | HTTPS FTP |
-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-PHE / | #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: 2.39 Å3/Da / Density % sol: 48.46 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG4000, Sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||||||||||
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: X26C / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48 Å / Num. all: 27246 / Num. obs: 27246 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4 % / Rmerge(I) obs: 0.201 / Num. unique all: 1361 / % possible all: 98.9 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 98.9 % |
-Processing
Software |
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Refinement | Resolution: 1.8→48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2118221.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.94 Å2 / ksol: 0.383 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 48 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 11.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.23 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.186 |