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Yorodumi- PDB-7jrx: Crystal structure of the R64F mutant of Bauhinia Bauhinioides com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jrx | ||||||
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Title | Crystal structure of the R64F mutant of Bauhinia Bauhinioides complexed with Bovine Chymotrypsin | ||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / Bovine Chymotrypsin / R64F / Bauhinia Bauhinioides Kallikrein Inhibitor / STRUCTURAL PROTEIN / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information chymotrypsin / endopeptidase inhibitor activity / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Bauhinia bauhinioides (plant) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.77 Å | ||||||
Authors | Li, M. / Wlodawer, A. / Gustchina, A. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Structural studies of complexes of kallikrein 4 with wild-type and mutated forms of the Kunitz-type inhibitor BbKI. Authors: Li, M. / Srp, J. / Mares, M. / Wlodawer, A. / Gustchina, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jrx.cif.gz | 179.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jrx.ent.gz | 145.9 KB | Display | PDB format |
PDBx/mmJSON format | 7jrx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jrx_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
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Full document | 7jrx_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 7jrx_validation.xml.gz | 37.3 KB | Display | |
Data in CIF | 7jrx_validation.cif.gz | 56.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/7jrx ftp://data.pdbj.org/pub/pdb/validation_reports/jr/7jrx | HTTPS FTP |
-Related structure data
Related structure data | 7jqkC 7jqnC 7jqoC 7jqvC 7jr1C 7jr2C C: citing same article (ref.) |
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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/peptide | Mass: 1253.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin #2: Protein | Mass: 13934.556 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin #3: Protein | Mass: 10074.495 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00766, chymotrypsin #4: Protein | Mass: 18130.498 Da / Num. of mol.: 2 / Mutation: R64F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bauhinia bauhinioides (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VEQ7 #5: 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: 2.21 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350, 0.2M Ammonium Acetate at pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→85.11 Å / Num. obs: 73379 / % possible obs: 95 % / Redundancy: 6.4 % / Rsym value: 0.096 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.77→1.8 Å / Num. unique obs: 2276 / Rsym value: 0.153 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.77→71.02 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.68 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 239.55 Å2 / Biso mean: 20.979 Å2 / Biso min: 6.46 Å2
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Refinement step | Cycle: final / Resolution: 1.77→71.02 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.77→1.811 Å / Rfactor Rfree error: 0
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