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Yorodumi- PDB-7jqn: Crystal structure of the R64M mutant of Bauhinia Bauhinioides Kal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jqn | ||||||
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Title | Crystal structure of the R64M mutant of Bauhinia Bauhinioides Kallikrein Inhibitor complexed with Human Kallikrein 4 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / HYDROLASE/INHIBITOR / Human Kallikrein 4 / Bauhinia Bauhiniordes Kallikrein Inhibitor / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information biomineral tissue development / amelogenesis / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / serine-type endopeptidase activity / proteolysis / extracellular space ...biomineral tissue development / amelogenesis / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Bauhinia bauhinioides (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 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 | 7jqn.cif.gz | 198.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jqn.ent.gz | 161.6 KB | Display | PDB format |
PDBx/mmJSON format | 7jqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jqn_validation.pdf.gz | 837.8 KB | Display | wwPDB validaton report |
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Full document | 7jqn_full_validation.pdf.gz | 843.1 KB | Display | |
Data in XML | 7jqn_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 7jqn_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/7jqn ftp://data.pdbj.org/pub/pdb/validation_reports/jq/7jqn | HTTPS FTP |
-Related structure data
Related structure data | 7jqkC 7jqoC 7jqvC 7jr1C 7jr2C 7jrxC 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules EI
#1: Protein | Mass: 23942.010 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4, EMSP1, PRSS17, PSTS / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y5K2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein | Mass: 18114.521 Da / Num. of mol.: 1 / Mutation: R64M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bauhinia bauhinioides (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VEQ7 |
-Non-polymers , 5 types, 646 molecules
#3: Chemical | #4: Chemical | ChemComp-CD / | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.23 Å3/Da / Density % sol: 61.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0 Ammonium Sulfate, 2%PEG400, 10mM CdCl2 pH 7.5 |
-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: Dec 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→86.99 Å / Num. obs: 982025 / % possible obs: 100 % / Redundancy: 11.3 % / Rsym value: 0.083 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 4314 / Rsym value: 0.854 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→62.67 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.078 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 123.2 Å2 / Biso mean: 26.675 Å2 / Biso min: 7.81 Å2
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Refinement step | Cycle: final / Resolution: 1.5→62.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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