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Yorodumi- PDB-3a3o: Crystal structure of complex between SA-subtilisin and Tk-propept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a3o | ||||||
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Title | Crystal structure of complex between SA-subtilisin and Tk-propeptide with deletion of the five C-terminal residues | ||||||
Components | (Tk-subtilisin) x 2 | ||||||
Keywords | HYDROLASE / subtilisin / propeptide / Thermococcus kodakaraensis / Protease / Secreted / Serine protease / Zymogen | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Tanaka, S. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Identification of the interactions critical for propeptide-catalyzed folding of Tk-subtilisin Authors: Tanaka, S. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a3o.cif.gz | 92.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a3o.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 3a3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/3a3o ftp://data.pdbj.org/pub/pdb/validation_reports/a3/3a3o | HTTPS FTP |
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-Related structure data
Related structure data | 3a3nC 3a3pC 2z30S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 33897.562 Da / Num. of mol.: 1 / Fragment: Residue in UNP 94-422 / Mutation: S324A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Plasmid: pET25b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P58502, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||||
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#2: Protein | Mass: 6988.176 Da / Num. of mol.: 1 / Fragment: Tk-propeptide, Residue in UNP 25-88 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Plasmid: pET25b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P58502 | ||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-ZN / | #5: 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: 1.99 Å3/Da / Density % sol: 38.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Sodium Cacodylate, 0.2M Zinc Acetate, 2%(w/v) PEG4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jul 2, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 26709 / % possible obs: 99.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 35.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 8.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z30 Resolution: 1.9→30.25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.815 / SU ML: 0.086 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 19.463 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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