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Yorodumi- PDB-1afq: CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN COMPLEXED WITH A S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1afq | ||||||
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Title | CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN COMPLEXED WITH A SYNTHETIC INHIBITOR | ||||||
Components | (BOVINE GAMMA- ...) x 3 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sugio, S. / Kashima, A. / Inoue, Y. / Maeda, I. / Nose, T. / Shimohigashi, Y. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 1998 Title: X-ray crystal structure of a dipeptide-chymotrypsin complex in an inhibitory interaction. Authors: Kashima, A. / Inoue, Y. / Sugio, S. / Maeda, I. / Nose, T. / Shimohigashi, Y. #1: Journal: Biochemistry / Year: 1991 Title: Gamma-Chymotrypsin is a Complex of Alpha-Chymotrypsin with its Own Autolysis Products Authors: Harel, M. / Su, C.-T. / Frolow, F. / Silman, I. / Sussman, J.L. #2: Journal: Int.J.Biol.Macromol. / Year: 1991 Title: Structure of Gamma-Chymotrypsin in the Range Ph 2.0 To Ph 10.5 Suggests that Gamma-Chymotrypsin is a Covalent Acyl-Enzyme Adduct at Low Ph Authors: Dixon, M.M. / Brennan, R.G. / Matthews, B.W. #3: Journal: Biochemistry / Year: 1989 Title: Is Gamma-Chymotrypsin a Tetrapeptide Acyl-Enzyme Adduct of Alpha-Chymotrypsin? Authors: Dixon, M.M. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1afq.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1afq.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 1afq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1afq_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1afq_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1afq_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 1afq_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/1afq ftp://data.pdbj.org/pub/pdb/validation_reports/af/1afq | HTTPS FTP |
-Related structure data
Related structure data | 1ab9SC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-BOVINE GAMMA- ... , 3 types, 3 molecules ABC
#1: Protein/peptide | Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin |
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#2: Protein | Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin |
#3: Protein | Mass: 10003.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00766, chymotrypsin |
-Non-polymers , 3 types, 130 molecules
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THERE ARE TWO INHIBITOR MOLECULES IN AN ASYMMETRIC UNIT. ONE (CHAIN C) IS BOUND TO SUBSTRATE ...THERE ARE TWO INHIBITOR MOLECULES IN AN ASYMMETRIC |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.18 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: GAMMA-CHYMOTRYPSIN CRYSTALS WERE SOAKED INTO A SOLUTION CONTAINING SATURATED INHIBITOR, 65% SATURATED AMMONIUM SULFATE AND 100 MM HEPES BUFFER (PH7.5) AT 293K FOR A MONTH. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 10, 1995 / Details: YALE MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→97.4 Å / Num. obs: 22647 / % possible obs: 98.1 % / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 4.09 / % possible all: 95.6 |
Reflection | *PLUS Num. measured all: 215467 |
Reflection shell | *PLUS % possible obs: 94.6 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 4.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AB9 Resolution: 1.8→5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: POSTERIORI / σ(F): 2
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Displacement parameters | Biso mean: 22.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.245 |