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Yorodumi- PDB-2z2z: Crystal structure of unautoprocessed form of Tk-subtilisin soaked... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z2z | ||||||
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Title | Crystal structure of unautoprocessed form of Tk-subtilisin soaked by 10mM CaCl2 | ||||||
Components | Tk-subtilisin precursor | ||||||
Keywords | HYDROLASE / subtilisin / Thermococcus kodakaraensis | ||||||
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: 1.87 Å | ||||||
Authors | Tanaka, S. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Four new crystal structures of Tk-subtilisin in unautoprocessed, autoprocessed and mature forms: insight into structural changes during maturation 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 | 2z2z.cif.gz | 95.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z2z.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 2z2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/2z2z ftp://data.pdbj.org/pub/pdb/validation_reports/z2/2z2z | HTTPS FTP |
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-Related structure data
Related structure data | 2z2xC 2z2yC 2z30C 2e1pS C: citing same article (ref.) 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
#1: Protein | Mass: 41078.031 Da / Num. of mol.: 1 / Fragment: UNP residues 28-422 / Mutation: S324A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Plasmid: pET25b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P58502, subtilisin | ||
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#2: Chemical | ChemComp-CA / #3: 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: 2.53 Å3/Da / Density % sol: 51.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 4.0M Sodium Formate, pH 8.0, 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: Oct 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→50 Å / Num. obs: 34961 / % possible obs: 99.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 45 |
Reflection shell | Resolution: 1.87→1.93 Å / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 7.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2E1P Resolution: 1.87→46.33 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.821 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.127 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.491 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→46.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.866→1.914 Å / Total num. of bins used: 20 /
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