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Yorodumi- PDB-2beb: X-ray structure of Asn to Thr mutant of Winged Bean Chymotrypsin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2beb | ||||||
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Title | X-ray structure of Asn to Thr mutant of Winged Bean Chymotrypsin inhibitor | ||||||
Components | Chymotrypsin inhibitor 3 | ||||||
Keywords | HYDROLASE INHIBITOR / Beta barrel / spacer / Mutant | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Psophocarpus tetragonolobus (winged bean) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Dattagupta, J.K. / Sen, U. / Dasgupta, J. / Khamrui, S. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Spacer Asn Determines the Fate of Kunitz (STI) Inhibitors, as Revealed by Structural and Biochemical Studies on WCI Mutants. Authors: Dasgupta, J. / Khamrui, S. / Dattagupta, J.K. / Sen, U. #1: Journal: Biochim.Biophys.Acta / Year: 2005 Title: Single mutation at P1 of a chymotrypsin inhibitor changes it to a trypsin inhibitor: X-ray structural (2.15 A) and biochemical basis. Authors: Khamrui, S. / Dasgupta, J. / Dattagupta, J.K. / Sen, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2beb.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2beb.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 2beb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/2beb ftp://data.pdbj.org/pub/pdb/validation_reports/be/2beb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20661.332 Da / Num. of mol.: 2 / Mutation: N17T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psophocarpus tetragonolobus (winged bean) Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P10822 #2: 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: 2.33 Å3/Da / Density % sol: 47.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 5% PEG 4000, 50 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→15 Å / Num. all: 9973 / Num. obs: 9349 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 84.4 Å2 / Rmerge(I) obs: 0.127 |
-Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→14.91 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1945470.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.0801 Å2 / ksol: 0.284467 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.81→14.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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