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Yorodumi- PDB-3btd: The Crystal Structures of the Complexes Between the Bovine Beta-T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3btd | ||||||
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Title | The Crystal Structures of the Complexes Between the Bovine Beta-Trypsin and Ten P1 Variants of BPTI. | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / TRYPSIN / BPTI / SERINE PROTEINASE / INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / serine protease inhibitor complex / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / cap snatching ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / serine protease inhibitor complex / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / cap snatching / virion component / serine-type endopeptidase inhibitor activity / protease binding / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / calcium ion binding / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Helland, R. / Otlewski, J. / Sundheim, O. / Dadlez, M. / Smalas, A.O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The crystal structures of the complexes between bovine beta-trypsin and ten P1 variants of BPTI. Authors: Helland, R. / Otlewski, J. / Sundheim, O. / Dadlez, M. / Smalas, A.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3btd.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3btd.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 3btd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3btd_validation.pdf.gz | 432.6 KB | Display | wwPDB validaton report |
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Full document | 3btd_full_validation.pdf.gz | 434.2 KB | Display | |
Data in XML | 3btd_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 3btd_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/3btd ftp://data.pdbj.org/pub/pdb/validation_reports/bt/3btd | HTTPS FTP |
-Related structure data
Related structure data | 3bteC 3btfC 3btgC 3bthC 3btkC 3btmC 3btqC 3bttC 3btwC 2ptcS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin | ||||
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#2: Protein | Mass: 6495.438 Da / Num. of mol.: 1 / Mutation: K15D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00974 | ||||
#3: Chemical | ChemComp-CA / | ||||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Compound details | P1 RESIDUE OF THE INHIBITOR IS MUTATED TO ASP | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.76 % | ||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 37 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. obs: 31159 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.31 / % possible all: 99.5 |
Reflection shell | *PLUS % possible obs: 99.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PTC Resolution: 1.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 1 Details: ENERGY TERMS OF THE INHIBITOR PEPTIDE SCISSILE BOND WERE SET TO ZERO DURING REFINEMENT
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Displacement parameters | Biso mean: 24.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2 Å / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.29 / Total num. of bins used: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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