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Yorodumi- PDB-3ofw: Crystal structure of recombinant Kunitz Type serine protease Inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ofw | ||||||
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Title | Crystal structure of recombinant Kunitz Type serine protease Inhibitor-1 from the Carribean sea anemone stichodactyla helianthus | ||||||
Components | Kunitz-type proteinase inhibitor SHPI-1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Kunitz Type / serine protease inhibitor / serine protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information nematocyst / aspartic-type endopeptidase inhibitor activity / serine-type endopeptidase inhibitor activity / extracellular region Similarity search - Function | ||||||
Biological species | Stichodactyla helianthus (sea anemone) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Garcia-Fernandez, R. / Redecke, L. / Pons, T. / Perbandt, M. / Talavera, A. / Gil, D. / Gonzalez, Y. / de los Angeles Chavez, M. / Betzel, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Structure of the recombinant BPTI/Kunitz-type inhibitor rShPI-1A from the marine invertebrate Stichodactyla helianthus. Authors: Garcia-Fernandez, R. / Pons, T. / Meyer, A. / Perbandt, M. / Gonzalez-Gonzalez, Y. / Gil, D. / de los Angeles Chavez, M. / Betzel, C. / Redecke, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ofw.cif.gz | 24 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ofw.ent.gz | 14.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ofw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/3ofw ftp://data.pdbj.org/pub/pdb/validation_reports/of/3ofw | HTTPS FTP |
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-Related structure data
Related structure data | 1shpS 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: 6624.505 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stichodactyla helianthus (sea anemone) / Production host: pichia pastoris (fungus) / References: UniProt: P31713 | ||
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#2: Chemical | #3: 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 Å3/Da / Density % sol: 58.94 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.7 M ammonium sulphate, 0.1 M Tris-HCl, 6% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.15K |
-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 10, 2010 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→35.358 Å / Num. obs: 3127 |
Reflection shell | Resolution: 2.5→2.64 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1SHP Resolution: 2.5→35.35 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.25 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 21.497 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→35.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.566 Å / Total num. of bins used: 20
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