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Open data
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Basic information
Entry | Database: PDB / ID: 2x8j | ||||||
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Title | Intracellular subtilisin precursor from B. clausii | ||||||
![]() | (INTRACELLULAR SUBTILISIN ...) x 2 | ||||||
![]() | HYDROLASE / SERINE PROTEASE / INTRACELLULAR PROTEINASE REGULATION | ||||||
Function / homology | ![]() serine-type endopeptidase activity / proteolysis / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vedodova, J. / Gamble, M. / Ariza, A. / Dodson, E. / Jones, D.D. / Wilson, K.S. | ||||||
![]() | ![]() Title: Crystal structure of an intracellular subtilisin reveals novel structural features unique to this subtilisin family. Authors: Vevodova, J. / Gamble, M. / Kunze, G. / Ariza, A. / Dodson, E. / Jones, D.D. / Wilson, K.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 | ![]() | 388.3 KB | Display | ![]() |
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PDB format | ![]() | 315.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2wv7C ![]() 2wwtSC 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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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-INTRACELLULAR SUBTILISIN ... , 2 types, 6 molecules ACDEFB
#1: Protein | Mass: 34717.746 Da / Num. of mol.: 5 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THESE CHAINS CONTAIN 1 OXIDISED CYS / Source: (gene. exp.) ![]() Description: ISOLATED FROM A NOVOZYMES STRAIN B. CLAUSII STRAIN -STRAIN NUMBER AVAILABLE ON REQUEST. Plasmid: PET22B / Production host: ![]() ![]() #2: Protein | | Mass: 34733.746 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THIS CHAIN CONTAINS 2 OXIDISED CYS / Source: (gene. exp.) ![]() Description: ISOLATED FROM A NOVOZYMES STRAIN B. CLAUSII STRAIN -STRAIN NUMBER AVAILABLE ON REQUEST. Plasmid: PET22B / Production host: ![]() ![]() |
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-Non-polymers , 4 types, 1515 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-1PE / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 250 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 250 TO ALA ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 48.5 % / Description: BASED ON PREVIOUSLY DETERMINED STRUCTURE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.9 Details: PEG 4K GLYCEROL 0.1M SODIUM CACODYLATE PH 5.9 0.2M SODIUM ACETATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 25, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9805 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→108.4 Å / Num. obs: 269002 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.56→1.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WWT Resolution: 1.56→75.98 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.958 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.09 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.843 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→75.98 Å
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Refine LS restraints |
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