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Yorodumi- PDB-1y7e: The Crystal Structure of Aminopeptidase I from Borrelia burgdorfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y7e | ||||||
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Title | The Crystal Structure of Aminopeptidase I from Borrelia burgdorferi B31 | ||||||
Components | Probable M18-family aminopeptidase 1 | ||||||
Keywords | HYDROLASE / aminopeptidase I / Borrelia burgdorferi B31 / yscI / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / zinc ion binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Borrelia burgdorferi (Lyme disease spirochete) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å | ||||||
Authors | Min, T. / Gorman, J. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of aminopeptidase I (yscI) from Borrelia burgdorferi Authors: Min, T. / Gorman, J. / Shapiro, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y7e.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y7e.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 1y7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/1y7e ftp://data.pdbj.org/pub/pdb/validation_reports/y7/1y7e | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 51893.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete) Gene: apeA / Plasmid: pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: Q45055, UniProt: P0C925*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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#2: 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: 3.24 Å3/Da / Density % sol: 61.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG 4k, 0.1M Bis-tris, 0.2M MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTAM Q315 / Detector: CCD / Date: Nov 4, 2004 |
Radiation | Monochromator: Si(111)double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. obs: 32224 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.094 |
Reflection shell | Resolution: 3.2→3.31 Å / Rmerge(I) obs: 0.233 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.2→19.81 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 203719.54 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10.3565 Å2 / ksol: 0.303453 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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