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Yorodumi- PDB-2fi5: Crystal structure of a BPTI variant (Cys38->Ser) in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fi5 | ||||||
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Title | Crystal structure of a BPTI variant (Cys38->Ser) in complex with trypsin | ||||||
Components |
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Keywords | hydrolase/hydrolase inhibitor / PROTEASE-INHIBITOR COMPLEX / 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 / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Zakharova, E. / Horvath, M.P. / Goldenberg, D.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Functional and structural roles of the Cys14-Cys38 disulfide of bovine pancreatic trypsin inhibitor. Authors: Zakharova, E. / Horvath, M.P. / Goldenberg, D.P. | ||||||
History |
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Remark 600 | HETEROGEN The residue IAS 115 in chain E is connected to residue 116 by a beta-peptide linkage. ...HETEROGEN The residue IAS 115 in chain E is connected to residue 116 by a beta-peptide linkage. This is a covalent bond between CG of IAS and N of the following residue in conformer A of the residues. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fi5.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fi5.ent.gz | 60.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/2fi5 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/2fi5 | HTTPS FTP |
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-Related structure data
Related structure data | 2fi3SC 2fi4C 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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3 |
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4 |
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5 |
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6 |
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7 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules EI
#1: Protein | Mass: 23325.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin |
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#2: Protein | Mass: 6511.502 Da / Num. of mol.: 1 / Mutation: C38S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid details: (Biochemistry 1988, 27, 2481-2489) / Plasmid: pTI103 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P00974 |
-Non-polymers , 5 types, 291 molecules
#3: Chemical | ChemComp-NA / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-EDO / #7: 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: 3.17 Å3/Da / Density % sol: 61.18 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5 M ammonium sulfate, 0.1 M HEPES, 0.02% sodium azide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: NONIUS KAPPA CCD2000 / Detector: CCD / Date: Mar 1, 2005 / Details: OSMIC CONFOCAL MAX-FLUX (GREEN) |
Radiation | Monochromator: OSMIC CONFOCAL MAX-FLUX (GREEN) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→20 Å / Num. all: 54726 / Num. obs: 52039 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5008 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2FI3 Resolution: 1.58→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber Details: Maximum-likelihood using measured intensities (mli) target implemented with CNS SOLVE 1.1.
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Solvent computation | Bsol: 18.4811 Å2 / ksol: 0.362438 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.58→20 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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