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Yorodumi- PDB-1lw6: Crystal Structure of the Complex of Subtilisin BPN' with Chymotry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lw6 | ||||||
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Title | Crystal Structure of the Complex of Subtilisin BPN' with Chymotrypsin Inhibitor 2 at 1.5 Angstrom Resolution | ||||||
Components |
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Keywords | HYDROLASE / SERINE PROTEASE / INHIBITOR | ||||||
Function / homology | Function and homology information subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / serine-type endopeptidase inhibitor activity / response to wounding / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus amyloliquefaciens (bacteria) Hordeum vulgare (barley) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Radisky, E.S. / Koshland JR., D.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: A clogged gutter mechanism for protease inhibitors. Authors: Radisky, E.S. / Koshland Jr., D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lw6.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lw6.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 1lw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lw6_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 1lw6_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 1lw6_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 1lw6_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/1lw6 ftp://data.pdbj.org/pub/pdb/validation_reports/lw/1lw6 | HTTPS FTP |
-Related structure data
Related structure data | 2sniS S: Starting model for refinement |
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Similar 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: 28381.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Plasmid: pser25 / Production host: Bacillus subtilis (bacteria) / Strain (production host): BG2036 / References: UniProt: P00782, subtilisin | ||
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#2: Protein | Mass: 7255.586 Da / Num. of mol.: 1 / Mutation: E45A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare (barley) / Strain: HIPROLY / Plasmid: pCI2ER1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01053 | ||
#3: Chemical | ChemComp-CA / | ||
#4: Chemical | ChemComp-SO4 / #5: 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: 2.56 Å3/Da / Density % sol: 51.91 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, ammonium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 21, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→29.66 Å / Num. all: 57529 / Num. obs: 57374 / % possible obs: 96.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.072 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 7527 / Rsym value: 0.34 / % possible all: 88.9 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 29.7 Å / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 88.9 % / Rmerge(I) obs: 0.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2SNI Resolution: 1.5→29.66 Å / σ(F): -3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 12.71 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→29.66 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 29.7 Å / Rfactor all: 0.17 / Rfactor Rfree: 0.188 / Rfactor Rwork: 0.169 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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