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Yorodumi- PDB-2ftm: Crystal structure of trypsin complexed with the BPTI variant (Tyr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ftm | ||||||
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Title | Crystal structure of trypsin complexed with the BPTI variant (Tyr35->Gly) | ||||||
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Hanson, W.M. / Horvath, M.P. / Goldenberg, D.P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Rigidification of a Flexible Protease Inhibitor Variant upon Binding to Trypsin. Authors: Hanson, W.M. / Domek, G.J. / Horvath, M.P. / Goldenberg, D.P. | ||||||
History |
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Remark 600 | Heterogen The residue IAS is connected to residue 116 by a beta-peptide linkage. This is a covalent ...Heterogen The residue IAS 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 | 2ftm.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ftm.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ftm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ftm_validation.pdf.gz | 461.5 KB | Display | wwPDB validaton report |
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Full document | 2ftm_full_validation.pdf.gz | 462.2 KB | Display | |
Data in XML | 2ftm_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 2ftm_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/2ftm ftp://data.pdbj.org/pub/pdb/validation_reports/ft/2ftm | HTTPS FTP |
-Related structure data
Related structure data | 2ftlC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#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: 6421.446 Da / Num. of mol.: 1 / Mutation: Y35G 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, 254 molecules
#3: Chemical | ChemComp-NA / | ||||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | #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: 61.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10 mM calcium chloride, 0.1 M HEPES, 2.0 M ammonium sulfate, 0.02% sodium azide; 20% ethylene glycol added upon harvesting and prior to freezing, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: Aug 4, 2002 / 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: 1.65→20 Å / Num. all: 45596 / Num. obs: 45459 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 4 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 5.6 / Num. unique all: 4357 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2PTC Resolution: 1.65→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber Details: maximum likelihood for measured reflection intensities (mli) target as implemented in CNS SOLVE 1.1
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Solvent computation | Bsol: 22.48 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→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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