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Yorodumi- PDB-3n55: SO1698 protein, an aspartic peptidase from Shewanella oneidensis. -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n55 | |||||||||
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Title | SO1698 protein, an aspartic peptidase from Shewanella oneidensis. | |||||||||
Components | (PeptidaseProtease) x 2 | |||||||||
Keywords | HYDROLASE / structural genomics / aspartic peptidase / autocatalysis / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Shewanella oneidensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.57 Å | |||||||||
Authors | Osipiuk, J. / Mulligan, R. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Characterization of member of DUF1888 protein family, self-cleaving and self-assembling endopeptidase. Authors: Osipiuk, J. / Mulligan, R. / Bargassa, M. / Hamilton, J.E. / Cunningham, M.A. / Joachimiak, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n55.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n55.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 3n55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/3n55 ftp://data.pdbj.org/pub/pdb/validation_reports/n5/3n55 | HTTPS FTP |
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-Related structure data
Related structure data | 3njfC 3njgC 3njhC 3njiC 3njjC 3njkC 3njlC 3njmC 3njnC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 12758.132 Da / Num. of mol.: 1 / Fragment: N-terminal domain 1-116 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1698 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EGA7 |
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#2: Protein/peptide | Mass: 1080.217 Da / Num. of mol.: 1 / Fragment: C-terminal domain 117-125 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1698 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EGA7 |
-Non-polymers , 4 types, 143 molecules
#3: Chemical | ChemComp-BME / |
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#4: Chemical | ChemComp-ACT / |
#5: Chemical | ChemComp-ZN / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | THE CHAIN-B PEPTIDE IS A PRODUCT OF AUTOCATALY |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 15% ETHANOL, 0.1 M MES BUFFER, 0.2 M ZINC ACETATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2005 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→32.9 Å / Num. obs: 27101 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.03 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.66 / Num. unique all: 2466 / Χ2: 0.765 / % possible all: 84.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.57→32.9 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 1.757 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.52 Å2 / Biso mean: 20.372 Å2 / Biso min: 7.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→32.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.569→1.61 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 1.0047 Å / Origin y: 21.124 Å / Origin z: 45.8209 Å
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