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Yorodumi- PDB-1y0r: Crystal structure of the tetrahedral aminopeptidase from P. horikoshii -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y0r | ||||||
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Title | Crystal structure of the tetrahedral aminopeptidase from P. horikoshii | ||||||
Components | Frv operon protein FrvX | ||||||
Keywords | HYDROLASE / Aminopeptidase domain / PDZ domain | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Groll, M. / Borissenko, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal Structure of TET Protease Reveals Complementary Protein Degradation Pathways in Prokaryotes Authors: Borissenko, L. / Groll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y0r.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y0r.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 1y0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/1y0r ftp://data.pdbj.org/pub/pdb/validation_reports/y0/1y0r | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is generated: x,y,z; x,-y,-z; -x,y,-z; -x,-y,z; z,x,y; -z,-x,y; z,-x,-y; -z,x,-y; y,z,x; -y,z,-x; -y,-z,x; y,-z,-x |
-Components
#1: Protein | Mass: 39071.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: prSet 6c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O59196 | ||||
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#2: Chemical | #3: Chemical | ChemComp-ARS / | #4: 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: 2.97 Å3/Da / Density % sol: 58.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.278, 1.2828, 1.05, 1.0 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 21, 2004 | |||||||||||||||
Radiation | Monochromator: Si(111) double crystal, non dispersive / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→99 Å / Num. all: 60213 / Num. obs: 59987 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 21.9 Å2 | |||||||||||||||
Reflection shell | Resolution: 1.7→1.73 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→14.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1245052.05 / 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: 63.6404 Å2 / ksol: 0.390604 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→14.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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