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- PDB-1f5r: RAT TRYPSINOGEN MUTANT COMPLEXED WITH BOVINE PANCREATIC TRYPSIN I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1f5r | ||||||
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Title | RAT TRYPSINOGEN MUTANT COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / TRYPSIN PRECURSOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / Neutrophil degranulation ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / Neutrophil degranulation / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / collagen catabolic process / trypsin / serine protease inhibitor complex / digestion / response to nutrient / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Pasternak, A. / White, A. / Cahoon, M. / Ringe, D. / Hedstrom, L. | ||||||
![]() | ![]() Title: The energetic cost of induced fit catalysis: Crystal structures of trypsinogen mutants with enhanced activity and inhibitor affinity. Authors: Pasternak, A. / White, A. / Jeffery, C.J. / Medina, N. / Cahoon, M. / Ringe, D. / Hedstrom, L. #1: ![]() Title: Comparison of Anionic and Cationic Trypsinogens: the Anionic Activation Domain is More Flexible in Solution and Differs in its Mode of BPTI Binding in the Crystal Structure Authors: Pasternak, A. / Ringe, D. / Hedstrom, L. #2: ![]() Title: Activating a Zymogen Without Proteolytic Processing: Mutation of Lys15 and Asn194 Activates Trypsinogen. Authors: Pasternak, A. / Liu, X. / Lin, T.-Y. / Hedstrom, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70 KB | Display | ![]() |
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PDB format | ![]() | 53.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 374.9 KB | Display | ![]() |
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Full document | ![]() | 374.6 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24736.742 Da / Num. of mol.: 1 / Mutation: DELTA-I16-V17, Q156K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 7337.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.63 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 22% PEG 3380, 300 mM Ammonium acetate, 100 mM Sodium acetate, , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 9, 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: 1.65→21.69 Å / Num. all: 35860 / Num. obs: 195481 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.45 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.56 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 1.92 % / Rmerge(I) obs: 0.242 / Num. unique all: 1494 / % possible all: 80.9 |
Reflection | *PLUS Num. obs: 35860 / Num. measured all: 195481 / Rmerge(I) obs: 0.05 |
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Processing
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Refinement | Resolution: 1.65→21.69 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.0572 Å2 / ksol: 0.340608 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→21.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor obs: 0.189 / Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.8 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.315 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.313 |