+Open data
-Basic information
Entry | Database: PDB / ID: 2zwo | ||||||
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Title | Crystal structure of Ca2 site mutant of Pro-S324A | ||||||
Components | Tk-subtilisin | ||||||
Keywords | HYDROLASE / subtilisin / Thermococcus kodakaraensis / calcium ion / Calcium / 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 kodakaraensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Takeuchi, Y. / Tanaka, S. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Requirement of a unique Ca(2+)-binding loop for folding of Tk-subtilisin from a hyperthermophilic archaeon. Authors: Takeuchi, Y. / 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 | 2zwo.cif.gz | 245.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zwo.ent.gz | 195.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/2zwo ftp://data.pdbj.org/pub/pdb/validation_reports/zw/2zwo | HTTPS FTP |
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-Related structure data
Related structure data | 2zwpC 2e1pS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 41348.312 Da / Num. of mol.: 3 / Mutation: D226A, S324A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakaraensis (archaea) / Plasmid: pET25b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P58502, subtilisin #2: Chemical | ChemComp-CA / #3: 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: 2.7 Å3/Da / Density % sol: 54.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES, 12%(w/v) PEG20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 19, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. obs: 82390 / % possible obs: 96.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.07→2.14 Å / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 1.3 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E1P Resolution: 2.07→46.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.322 / SU ML: 0.108 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.17 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.849 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→46.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.069→2.123 Å / Total num. of bins used: 20
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