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Yorodumi- PDB-3viv: 1510-N membrane-bound stomatin-specific protease K138A mutant in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3viv | ||||||
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Title | 1510-N membrane-bound stomatin-specific protease K138A mutant in complex with a substrate peptide | ||||||
Components |
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Keywords | HYDROLASE/PROTEIN BINDING / protein-peptide complex / alpha / beta motif / protease / membrane protein stomatin / HYDROLASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) Pyrococcus horikoshii OT3 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å | ||||||
Authors | Yokoyama, H. / Matsui, I. / Fujii, S. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Crystal structure of a membrane stomatin-specific protease in complex with a substrate Peptide Authors: Yokoyama, H. / Takizawa, N. / Kobayashi, D. / Matsui, I. / Fujii, S. #1: Journal: J.SYNCHROTRON RADIAT. / Year: 2008 Title: Novel dimer structure of a membrane-bound protease with a catalytic Ser-Lys dyad and its linkage to stomatin. Authors: Yokoyama, H. / Hamamatsu, S. / Fujii, S. / Matsui, I. #2: Journal: J.Mol.Biol. / Year: 2006 Title: Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii. Authors: Yokoyama, H. / Matsui, E. / Akiba, T. / Harata, K. / Matsui, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3viv.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3viv.ent.gz | 150.2 KB | Display | PDB format |
PDBx/mmJSON format | 3viv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/3viv ftp://data.pdbj.org/pub/pdb/validation_reports/vi/3viv | HTTPS FTP |
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-Related structure data
Related structure data | 3bppS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 25368.025 Da / Num. of mol.: 2 / Fragment: Residues 16-236 / Mutation: K138A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1510 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: O59179 #2: Protein/peptide | | Mass: 1158.473 Da / Num. of mol.: 1 / Fragment: Residues 234-243 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Pyrococcus horikoshii OT3 (archaea) / References: UniProt: O59180 |
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-Non-polymers , 4 types, 150 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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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: 2.75 Å3/Da / Density % sol: 55.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.0M imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 19, 2010 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. obs: 27554 / % possible obs: 98.7 % / Redundancy: 10.6 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 67.9 |
Reflection shell | Resolution: 2.25→2.33 Å / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 9.8 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BPP Resolution: 2.25→19.74 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 13.102 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.222 / 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: 81.3 Å2 / Biso mean: 52.386 Å2 / Biso min: 11.17 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.253→2.311 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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