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Open data
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Basic information
Entry | Database: PDB / ID: 2z2y | ||||||
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Title | Crystal structure of autoprocessed form of Tk-subtilisin | ||||||
![]() | (Tk-subtilisin) x 2 | ||||||
![]() | HYDROLASE / subtilisin / Thermococcus kodakaraensis / autoprocessed | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tanaka, S. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.8 KB | Display | ![]() |
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PDB format | ![]() | 128 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2z2xC ![]() 2z2zC ![]() 2z30C ![]() 2e1pS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32900.500 Da / Num. of mol.: 2 / Mutation: S324C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 7084.432 Da / Num. of mol.: 2 / Fragment: propeptide domain, UNP Residues 29-93 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.95 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Sodium Cacodylate, 0.2M Zinc Acetate, 2% (w/v) PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. obs: 65891 / % possible obs: 96.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.89→1.96 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.2 / % possible all: 85.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2E1P Resolution: 1.89→46.88 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.719 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.125 / 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: 24.071 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→46.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.892→1.942 Å / Total num. of bins used: 20
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