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Open data
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Basic information
Entry | Database: PDB / ID: 2z58 | ||||||
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Title | Crystal structure of G56W-propeptide:S324A-subtilisin complex | ||||||
![]() | (Tk-subtilisin) x 2 | ||||||
![]() | HYDROLASE / propeptide / subtilisin / Thermococcus kodakaraensis | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Pulido, M.A. / Tanaka, S. / Sringiew, C. / You, D.J. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
![]() | ![]() Title: Requirement of left-handed glycine residue for high stability of the Tk-subtilisin propeptide as revealed by mutational and crystallographic analyses Authors: Pulido, M.A. / Tanaka, S. / Sringiew, C. / You, D.J. / 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 | ![]() | 89 KB | Display | ![]() |
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PDB format | ![]() | 65.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.2 KB | Display | ![]() |
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Full document | ![]() | 451.7 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2z56C ![]() 2z57C ![]() 2e1pS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32868.438 Da / Num. of mol.: 1 / Fragment: Mature domain, Residue 81-398 / Mutation: S324A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 7327.693 Da / Num. of mol.: 1 / Fragment: Propeptide domain, Residue 4-69 / Mutation: G56W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1M Sodium Acetate (pH 5.0), 10%(v/v) Isopropanol, 0.2M Zinc Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRUKER SMART 6500 / Detector: CCD / Date: Nov 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 27551 / % possible obs: 97.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 33.6 |
Reflection shell | Resolution: 1.86→1.93 Å / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 4.6 / % possible all: 73.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2E1P Resolution: 1.88→50 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.895 / SU B: 4.304 / SU ML: 0.131 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.149 / 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: 22.113 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.881→1.93 Å / Total num. of bins used: 20 /
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