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Yorodumi- PDB-1y3f: Crystal structure of the complex of subtilisin BPN' with chymotry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y3f | ||||||
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Title | Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 F69A mutant | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / serine protease / inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / response to wounding / serine-type endopeptidase inhibitor activity / 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: 1.72 Å | ||||||
Authors | Radisky, E.S. / Lu, C.J. / Kwan, G. / Koshland Jr., D.E. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Role of the intramolecular hydrogen bond network in the inhibitory power of chymotrypsin inhibitor 2 Authors: Radisky, E.S. / Lu, C.J. / Kwan, G. / 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 | 1y3f.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y3f.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 1y3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/1y3f ftp://data.pdbj.org/pub/pdb/validation_reports/y3/1y3f | HTTPS FTP |
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-Related structure data
Related structure data | 1y1kC 1y33C 1y34C 1y3bC 1y3cC 1y3dC 1y48C 1y4aC 1y4dC 1tm3S 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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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules EI
#1: Protein | Mass: 28381.396 Da / Num. of mol.: 1 / Mutation: C-terminal 6-His tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: apr / Plasmid: pSer25 / Production host: Bacillus subtilis (bacteria) / Strain (production host): BG2036 / References: UniProt: P00782, subtilisin |
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#2: Protein | Mass: 7207.504 Da / Num. of mol.: 1 / Mutation: initiating Met, F69A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare (barley) / Plasmid: pCI2F69A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q40059 |
-Non-polymers , 5 types, 498 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | ChemComp-NA / | ||||
#5: Chemical | #6: Chemical | #7: 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: 2.7 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: sodium citrate, isopropanol, PEG 4000, 3% xylitol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→81.65 Å / Num. all: 51924 / Num. obs: 49329 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rsym value: 0.101 / Net I/σ(I): 10.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TM3 Resolution: 1.72→81.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.863 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.315 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→81.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.765 Å / Total num. of bins used: 20 /
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