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Yorodumi- PDB-3d65: Crystal structure of Textilinin-1, a Kunitz-type serine protease ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d65 | ||||||
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Title | Crystal structure of Textilinin-1, a Kunitz-type serine protease inhibitor from the Australian Common Brown snake venom, in complex with trypsin | ||||||
Components |
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Keywords | HYDROLASE INHIBITOR/HYDROLASE / Serine protease inhibitor / trypsin / blood / coagulation / Calcium / Digestion / Hydrolase / Metal-binding / Protease / Secreted / Serine protease / Zymogen / HYDROLASE INHIBITOR-HYDROLASE COMPLEX | ||||||
Function / homology | Function and homology information suppression of blood coagulation in another organism / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / toxin activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis ...suppression of blood coagulation in another organism / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / toxin activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudonaja textilis textilis (cobra) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Millers, E.-K.I. / Masci, P.P. / Lavin, M.F. / de Jersey, J. / Guddat, L.W. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Textilinin-1, a Kunitz-type serine protease inhibitor from the Australian Common Brown snake venom, in complex with trypsin Authors: Millers, E.-K.I. / Lavin, M.F. / de Jersey, J. / Masci, P.P. / Guddat, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d65.cif.gz | 72.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d65.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 3d65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d65_validation.pdf.gz | 435.3 KB | Display | wwPDB validaton report |
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Full document | 3d65_full_validation.pdf.gz | 437.4 KB | Display | |
Data in XML | 3d65_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 3d65_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/3d65 ftp://data.pdbj.org/pub/pdb/validation_reports/d6/3d65 | HTTPS FTP |
-Related structure data
Related structure data | 3ptnS 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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Unit cell |
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-Components
#1: Protein | Mass: 6454.175 Da / Num. of mol.: 1 / Fragment: residues 3-59 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudonaja textilis textilis (cobra) / Production host: Escherichia coli (E. coli) / References: UniProt: Q90WA1 |
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#2: Protein | Mass: 23324.287 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 |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Sequence details | THIS COORDINATE SECTION IS USED NON-SEQUENTIAL RESIDUE NUMBERING. TRYPSIN IS NUMBERED ACCORDING TO ...THIS COORDINATE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES-Na, 1.4M tri-sodium citrate dehydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 16, 2006 / Details: Confocal X-ray optics Osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→50 Å / Num. all: 49994 / Num. obs: 49994 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.85 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.63→1.69 Å / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 11.47 / Num. unique all: 4534 / Rsym value: 0.494 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PTN Resolution: 1.64→37.42 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.259 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.092 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.218 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→37.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.639→1.681 Å / Total num. of bins used: 20
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