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Yorodumi- PDB-3njm: P117A mutant of SO1698 protein, an aspartic peptidase from Shewan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3njm | ||||||
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Title | P117A mutant of SO1698 protein, an aspartic peptidase from Shewanella oneidensis. | ||||||
Components | PeptidaseProtease | ||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / ASPARTIC PEPTIDASE / AUTOCATALYSIS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG | ||||||
Function / homology | DP-EP family / DP-EP family / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta / metal ion binding / Autocatalytic aspartic peptidase Function and homology information | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Osipiuk, J. / Mulligan, R. / Bargassa, M. / 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 | 3njm.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3njm.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 3njm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/3njm ftp://data.pdbj.org/pub/pdb/validation_reports/nj/3njm | HTTPS FTP |
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-Related structure data
Related structure data | 3n55SC 3njfC 3njgC 3njhC 3njiC 3njjC 3njkC 3njlC 3njnC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13700.505 Da / Num. of mol.: 1 / Mutation: P117A 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: 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: 3.51 Å3/Da / Density % sol: 64.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Bis-Tris buffer, 0.3 M magnesium formate, pH 5.5, 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-BM / Wavelength: 0.9792 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Nov 23, 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: 1.64→28.7 Å / Num. all: 23667 / Num. obs: 23667 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.048 / Χ2: 0.745 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 2.25 / Num. unique all: 1172 / Χ2: 0.614 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3N55 Resolution: 1.64→28.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.644 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.07 / ESU R Free: 0.073 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.04 Å2 / Biso mean: 27.996 Å2 / Biso min: 8.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→28.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.641→1.684 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 50.2085 Å / Origin y: 7.407 Å / Origin z: 38.0563 Å
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