+Open data
-Basic information
Entry | Database: PDB / ID: 1c9m | ||||||
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Title | BACILLUS LENTUS SUBTILSIN (SER 87) N76D/S103A/V104I | ||||||
Components | SERINE PROTEASE | ||||||
Keywords | HYDROLASE / SERINE PROTEASE / SUBTILISIN / SITE-SPECIFIC VARIANT / ALTERED FLEXIBILITY | ||||||
Function / homology | Function and homology information subtilisin / sporulation resulting in formation of a cellular spore / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus lentus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.67 Å | ||||||
Authors | Bott, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Engineered Bacillus lentus subtilisins having altered flexibility. Authors: Graycar, T. / Knapp, M. / Ganshaw, G. / Dauberman, J. / Bott, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c9m.cif.gz | 59.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c9m.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 1c9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c9m_validation.pdf.gz | 377.8 KB | Display | wwPDB validaton report |
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Full document | 1c9m_full_validation.pdf.gz | 383.8 KB | Display | |
Data in XML | 1c9m_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1c9m_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/1c9m ftp://data.pdbj.org/pub/pdb/validation_reports/c9/1c9m | HTTPS FTP |
-Related 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: 26871.576 Da / Num. of mol.: 1 / Mutation: N76D, S103A, V104I FROM NATIVE (SER 87) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus lentus (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: P29600, subtilisin | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.96 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.9 Details: SODIUM ACTETATE, CALCIUM CHLORIDE, AMMONIUM SULFATE ,PHENYLMETHYLSULFANYL- FLOURIDE, pH 5.9, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 10, 1993 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→10 Å / Num. all: 26797 / Num. obs: 26797 / % possible obs: 91 % / Observed criterion σ(F): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 |
Reflection shell | Resolution: 1.67→10 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 / % possible all: 91 |
Reflection | *PLUS Rmerge(I) obs: 0.04 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.67→10 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.67→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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