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Yorodumi- PDB-3rdz: Crystal Structure of rBTI-trypsin complex at 2.26 angstrom resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rdz | ||||||
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Title | Crystal Structure of rBTI-trypsin complex at 2.26 angstrom resolution | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / serine protease inhibitor / potato inhibitor I / trypsin inhibitor / trypsin / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / response to wounding / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Fagopyrum esculentum (common buckwheat) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.262 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 | 3rdz.cif.gz | 126.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rdz.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 3rdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rdz_validation.pdf.gz | 449.6 KB | Display | wwPDB validaton report |
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Full document | 3rdz_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 3rdz_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 3rdz_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/3rdz ftp://data.pdbj.org/pub/pdb/validation_reports/rd/3rdz | HTTPS FTP |
-Related structure data
Related structure data | 3rdyC 1vbwS 2cmyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Purchased from AppliChem / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin #2: Protein | Mass: 9019.240 Da / Num. of mol.: 2 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 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15% (w/v) PEG 3350, 200mM magnesium chloride, 100mM Tris-HCl (pH 9.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 20, 2009 |
Radiation | Monochromator: X-Ray Generator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→20 Å / Num. all: 26331 / Num. obs: 26279 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 181.7 |
Reflection shell | Resolution: 2.26→2.34 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 31 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2CMY, 1VBW Resolution: 2.262→20 Å / FOM work R set: 0.8267 / SU ML: 0.31 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 24.02 / 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: 44.032 Å2 / ksol: 0.399 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.262→20 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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