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Yorodumi- PDB-1y4d: Crystal structure of the complex of subtilisin BPN' with chymotry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y4d | ||||||
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Title | Crystal structure of the complex of subtilisin BPN' with chymotrypsin inhibitor 2 M59R/E60S 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: 2 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 | 1y4d.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y4d.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 1y4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/1y4d ftp://data.pdbj.org/pub/pdb/validation_reports/y4/1y4d | HTTPS FTP |
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-Related structure data
Related structure data | 1y1kC 1y33C 1y34C 1y3bC 1y3cC 1y3dC 1y3fC 1y48C 1y4aC 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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Unit cell |
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-Components
#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: 7267.563 Da / Num. of mol.: 1 / Mutation: initiating Met, M59R/E60S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare (barley) / Plasmid: PCI2M59R-E60S / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q40059 |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-NA / |
#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: 2.3 Å3/Da / Density % sol: 45.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: potassium phosphate, PEG 8000, pH 4.5, 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 4, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→32.55 Å / Num. all: 22160 / Num. obs: 22160 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rsym value: 0.157 / Net I/σ(I): 7.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TM3 Resolution: 2→32.55 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.621 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.18 / 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: 26.581 Å2
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Refinement step | Cycle: LAST / Resolution: 2→32.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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