+Open data
-Basic information
Entry | Database: PDB / ID: 1dpo | ||||||
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Title | STRUCTURE OF RAT TRYPSIN | ||||||
Components | TRYPSIN | ||||||
Keywords | SERINE PROTEASE / HYDROLASE / DIGESTION / PANCREAS / ZYMOGEN / MULTIGENE FAMILY | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Collagen degradation / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Collagen degradation / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Rattus rattus (black rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.59 Å | ||||||
Authors | Stroud, R.M. | ||||||
Citation | Journal: Proteins / Year: 1991 Title: 1.59 A structure of trypsin at 120 K: comparison of low temperature and room temperature structures. Authors: Earnest, T. / Fauman, E. / Craik, C.S. / Stroud, R. #1: Journal: Science / Year: 1987 Title: The Three-Dimensional Structure of Asn102 Mutant of Trypsin: Role of Asp102 in Serine Protease Catalysis Authors: Sprang, S. / Standing, T. / Fletterick, R.J. / Stroud, R.M. / Finer-Moore, J. / Xuong, N.H. / Hamlin, R. / Rutter, W.J. / Craik, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dpo.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dpo.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/1dpo ftp://data.pdbj.org/pub/pdb/validation_reports/dp/1dpo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
#1: Protein | Mass: 23830.902 Da / Num. of mol.: 1 / Mutation: S195C Source method: isolated from a genetically manipulated source Details: ANIONIC TRYPSIN / Source: (gene. exp.) Rattus rattus (black rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P00763, trypsin | ||||
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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | #4: Chemical | #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: 3.26 Å3/Da / Density % sol: 62.29 % / Description: DATA COLLECTED AT 120 DEGREES K | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1988 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→100 Å / Num. obs: 41613 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.1051 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 1.59→1.68 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.287 / % possible all: 81.6 |
Reflection | *PLUS Rmerge(I) obs: 0.1051 |
-Processing
Software |
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Refinement | Resolution: 1.59→12 Å / σ(F): 0
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Displacement parameters | Biso mean: 9.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→12 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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