+Open data
-Basic information
Entry | Database: PDB / ID: 2wwt | ||||||
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Title | Intracellular subtilisin precursor from B. clausii | ||||||
Components | INTRACELLULAR SUBTILISIN PROTEASE | ||||||
Keywords | HYDROLASE / INTRACELLULAR PROTEINASE REGULATION | ||||||
Function / homology | Function and homology information serine-type endopeptidase activity / proteolysis / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS CLAUSII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Vevodova, J. / Gamble, M. / Ariza, A. / Dodson, E. / Jones, D.D. / Wilson, K.S. | ||||||
Citation | Journal: Structure / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wwt.cif.gz | 660.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wwt.ent.gz | 547.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/2wwt ftp://data.pdbj.org/pub/pdb/validation_reports/ww/2wwt | HTTPS FTP |
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-Related structure data
Related structure data | 2wv7C 2x8jC 1yjcS 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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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
#1: Protein | Mass: 34944.020 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS CLAUSII (bacteria) Description: ISOLATED FROM A NOVOZYMES STRAIN OF B. CLAUSII. STRAIN NUMBER AVAILABLE ON REQUEST. Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: D0AB41, subtilisin #2: Chemical | ChemComp-NA / #3: Water | ChemComp-HOH / | 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1M BISTRIS, PH6.5, 0.1 M NACL, 1.5M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9762 | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 25, 2006 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.68→60.8 Å / Num. obs: 49303 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.6 | |||||||||||||||
Reflection shell | Resolution: 2.68→2.83 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YJC Resolution: 2.68→105.57 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.836 / SU B: 32.633 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R Free: 0.078 / 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: 39.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.68→105.57 Å
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Refine LS restraints |
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