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Yorodumi- PDB-1p2j: Structural consequences of accommodation of four non-cognate amin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p2j | ||||||
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Title | Structural consequences of accommodation of four non-cognate amino-acid residues in the S1 pocket of bovine trypsin and chymotrypsin | ||||||
Components |
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Keywords | hydrolase/hydrolase inhibitor / trypsin / chymotrypsin / serine proteinase / bovine pancreatic trypsin inhibitor / protein-protein interaction / non-cognate binding / S1 pocket / primary specificity / crystal structure / 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: 1.35 Å | ||||||
Authors | Helland, R. / Czapinska, H. / Leiros, I. / Olufsen, M. / Otlewski, J. / Smalaas, A.O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structural consequences of accommodation of four non-cognate amino acid residues in the S1 pocket of bovine trypsin and chymotrypsin. Authors: Helland, R. / Czapinska, H. / Leiros, I. / Olufsen, M. / Otlewski, J. / Smalaas, A.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p2j.cif.gz | 124 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p2j.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 1p2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p2j_validation.pdf.gz | 436.3 KB | Display | wwPDB validaton report |
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Full document | 1p2j_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | 1p2j_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1p2j_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/1p2j ftp://data.pdbj.org/pub/pdb/validation_reports/p2/1p2j | HTTPS FTP |
-Related structure data
Related structure data | 1p2iC 1p2kC 1p2mC 1p2nC 1p2oC 1p2qC 3btgS C: citing same article (ref.) S: Starting model for refinement |
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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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3 |
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Unit cell |
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Components on special symmetry positions |
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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: 6493.508 Da / Num. of mol.: 1 / Mutation: K15L, M52L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Description: T7 PROMOTER / Plasmid: pAED4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00974 | ||
#3: Chemical | ChemComp-CA / | ||
#4: Chemical | ChemComp-SO4 / #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: 2.88 Å3/Da / Density % sol: 56.97 % |
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50% ammonium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9312 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9312 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→14.98 Å / Num. all: 77696 / Num. obs: 77696 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 13.81 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 2.4 / Num. unique all: 77728 / Rsym value: 0.209 / % possible all: 64.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3btg Resolution: 1.35→8 Å / Isotropic thermal model: Anisotropical / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Refinement was done using both CNS and SHELX
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Displacement parameters | Biso mean: 18.01 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.17 Å / Luzzati sigma a obs: 0.16 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→8 Å
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Refine LS restraints |
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