+Open data
-Basic information
Entry | Database: PDB / ID: 1qq9 | ||||||
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Title | STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH METHIONINE | ||||||
Components | AMINOPEPTIDASE | ||||||
Keywords | HYDROLASE / DOUBLE-ZINC METALLOPROTEINAZE / 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 / Resolution: 1.53 Å | ||||||
Authors | Gilboa, R. / Greenblatt, H.M. / Perach, M. / Spungin-Bialik, A. / Lessel, U. / Schomburg, D. / Blumberg, S. / Shoham, G. | ||||||
Citation | 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. #1: 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. #2: 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. #3: Journal: Eur.J.Biochem. / Year: 1996 Title: Aminopeptidase from Streptomyces 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 | 1qq9.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qq9.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qq9_validation.pdf.gz | 364.5 KB | Display | wwPDB validaton report |
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Full document | 1qq9_full_validation.pdf.gz | 364.5 KB | Display | |
Data in XML | 1qq9_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1qq9_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/1qq9 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/1qq9 | 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
#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-MET / | #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: 47.74 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: PEG 4000, AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion / Details: Greenblatt, H.M., (1997) J.Mol.Biol., 265, 620. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.083 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 16, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.083 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→35 Å / Num. all: 42869 / Num. obs: 42630 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 3 % / Rmerge(I) obs: 0.203 / % possible all: 69.8 |
Reflection shell | *PLUS % possible obs: 69.8 % |
-Processing
Software |
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Refinement | Resolution: 1.53→32 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1937578.64 / 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: 41.8 Å2 / ksol: 0.322 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.53→32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.63 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.217 / % reflection Rfree: 10.6 % / Rfactor Rwork: 0.181 |