+Open data
-Basic information
Entry | Database: PDB / ID: 1scj | ||||||
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Title | CRYSTAL STRUCTURE OF SUBTILISIN-PROPEPTIDE COMPLEX | ||||||
Components | (SUBTILISIN ESubtilisin) x 2 | ||||||
Keywords | HYDROLASE / SUBTILISIN E - PROPEPTIDE / SERINE PROTEASE | ||||||
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 subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Berman, H.M. / Jain, S.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: The crystal structure of an autoprocessed Ser221Cys-subtilisin E-propeptide complex at 2.0 A resolution. Authors: Jain, S.C. / Shinde, U. / Li, Y. / Inouye, M. / Berman, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1scj.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1scj.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 1scj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sc/1scj ftp://data.pdbj.org/pub/pdb/validation_reports/sc/1scj | HTTPS FTP |
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-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: 27748.625 Da / Num. of mol.: 1 / Mutation: S221C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): DE3-BL2 / References: UniProt: P04189, subtilisin | ||
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#2: Protein | Mass: 7980.167 Da / Num. of mol.: 1 / Mutation: S221C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): DE3-BL2 / References: UniProt: P04189, subtilisin | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 30444 / % possible obs: 87 % / Observed criterion σ(I): 3 / Redundancy: 7.8 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.075 / Net I/σ(I): 34 |
Reflection shell | Resolution: 2→2.13 Å / Rsym value: 0.132 / % possible all: 60 |
Reflection | *PLUS Num. measured all: 248934 / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS Rmerge(I) obs: 0.138 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CSE AND 1SPB Resolution: 2→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 513244.98 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 Details: BULK SOLVENT MODEL USED DATA CUTOFF HIGH (ABS(F)) : 513244.98 DATA CUTOFF LOW (ABS(F)) : 0.000000
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Displacement parameters | Biso mean: 19.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.15 |