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Yorodumi- PDB-1gg6: CRYSTAL STRUCTURE OF GAMMA CHYMOTRYPSIN WITH N-ACETYL-PHENYLALANI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gg6 | ||||||
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Title | CRYSTAL STRUCTURE OF GAMMA CHYMOTRYPSIN WITH N-ACETYL-PHENYLALANINE TRIFLUOROMETHYL KETONE BOUND AT THE ACTIVE SITE | ||||||
Components | (GAMMA CHYMOTRYPSIN) x 3 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / CHYMOTRYPSIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information chymotrypsin / serpin family protein binding / digestion / serine protease inhibitor complex / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.4 Å | ||||||
Authors | Neidhart, D. / Wei, Y. / Cassidy, C. / Lin, J. / Cleland, W.W. / Frey, P.A. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Correlation of low-barrier hydrogen bonding and oxyanion binding in transition state analogue complexes of chymotrypsin. Authors: Neidhart, D. / Wei, Y. / Cassidy, C. / Lin, J. / Cleland, W.W. / Frey, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gg6.cif.gz | 68.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gg6.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gg6_validation.pdf.gz | 532.4 KB | Display | wwPDB validaton report |
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Full document | 1gg6_full_validation.pdf.gz | 532.5 KB | Display | |
Data in XML | 1gg6_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1gg6_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/1gg6 ftp://data.pdbj.org/pub/pdb/validation_reports/gg/1gg6 | HTTPS FTP |
-Related 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
-Protein/peptide , 1 types, 1 molecules A
#1: Protein/peptide | Mass: 996.223 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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-Protein , 2 types, 2 molecules BC
#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 |
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#3: Protein | Mass: 10074.495 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 , 5 types, 342 molecules
#4: Chemical | #5: Chemical | ChemComp-APL / | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-APF / | #8: Water | ChemComp-HOH / | |
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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: 2.28 Å3/Da / Density % sol: 46.15 % | |||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: ammonium sulfate, potassium phosphate, pH 7.0, vapor diffusion, temperature 298.0K | |||||||||||||||
Crystal grow | *PLUS | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Nov 29, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 45082 / Num. obs: 42041 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.027 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.118 / % possible all: 75.8 |
Reflection | *PLUS Num. obs: 45082 |
Reflection shell | *PLUS % possible obs: 75.8 % |
-Processing
Software |
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Refinement | Resolution: 1.4→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: Initial coordinates for this structure were derived from the model of G. Cohen et al. (PDB entry 2GCH). Secondary structure elements and sequence data are identical to those of entry 2GCH ...Details: Initial coordinates for this structure were derived from the model of G. Cohen et al. (PDB entry 2GCH). Secondary structure elements and sequence data are identical to those of entry 2GCH except that the use of cryocrystallography techniques and the extended resolution of the current study permitted assignment of coordinates to residues 149 and 150, which are adjacent to a natural excission site. Initial phases were derived from the 2GCH model. A previous entry by Brady et al. (PDB entry 6gch) describes an identical complex determined by crystal structure analysis at lower resolution (2.1 Angstrom). More accurate determination of hydrogen bonding distances within the catalytic triad motivated the current study.
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Refinement step | Cycle: LAST / Resolution: 1.4→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.5 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.175 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.4 |