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Yorodumi- PDB-3rdy: Crystal Structure of buckwheat trypsin inhibitor rBTI at 1.84 ang... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rdy | ||||||
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Title | Crystal Structure of buckwheat trypsin inhibitor rBTI at 1.84 angstrom resolution | ||||||
Components | BWI-1=PROTEASE inhibitor/trypsin inhibitor | ||||||
Keywords | HYDROLASE INHIBITOR / serine protease inhibitor / potato inhibitor I / trypsin inhibitor / trypsin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Fagopyrum esculentum (common buckwheat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Wang, L.F. / Li, M. / Chang, W.R. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Conformational Changes of rBTI from Buckwheat upon Binding to Trypsin: Implications for the Role of the P(8)' Residue in the Potato Inhibitor I Family Authors: Wang, L.F. / Zhao, F. / Li, M. / Zhang, H. / Gao, Y. / Cao, P. / Pan, X. / Wang, Z. / Chang, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rdy.cif.gz | 27.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rdy.ent.gz | 16.7 KB | Display | PDB format |
PDBx/mmJSON format | 3rdy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rdy_validation.pdf.gz | 413.7 KB | Display | wwPDB validaton report |
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Full document | 3rdy_full_validation.pdf.gz | 413.7 KB | Display | |
Data in XML | 3rdy_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 3rdy_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/3rdy ftp://data.pdbj.org/pub/pdb/validation_reports/rd/3rdy | HTTPS FTP |
-Related structure data
Related structure data | 3rdzSC 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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Unit cell |
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-Components
#1: Protein | Mass: 9019.240 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fagopyrum esculentum (common buckwheat) Gene: BWI-1, Edn1 / Plasmid: QIA express pQE-31 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9S9F3 |
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#2: 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: 2.5 Å3/Da / Density % sol: 50.75 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: 24% (w/v) PEG MME 2000, 220mM ammonium sulfate, 100mM sodium acetate (pH 4.4), 100mM sodium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Dec 3, 2009 |
Radiation | Monochromator: Si(111) double flat-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→15 Å / Num. all: 8360 / Num. obs: 8344 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 24.1 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 46.4 |
Reflection shell | Resolution: 1.84→1.91 Å / Redundancy: 23.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RDZ Resolution: 1.84→14.464 Å / FOM work R set: 0.856 / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 20.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.987 Å2 / ksol: 0.393 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→14.464 Å
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Refine LS restraints |
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LS refinement shell |
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