+Open data
-Basic information
Entry | Database: PDB / ID: 7jod | ||||||
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Title | Crytsal structure of BbKI complexed with Human Kallikrein 4 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / inhibitor / PLANT PROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information amelogenesis / endopeptidase inhibitor activity / extracellular matrix disassembly / protein catabolic process / serine-type endopeptidase activity / proteolysis / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Bauhinia bauhinioides (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å | ||||||
Authors | Li, M. / Wlodawer, A. / Gustchina, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / 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 | 7jod.cif.gz | 205 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jod.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 7jod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/7jod ftp://data.pdbj.org/pub/pdb/validation_reports/jo/7jod | HTTPS FTP |
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-Related structure data
Related structure data | 7joeC 7josC 7jowC 4k8yS 6dwfS 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules EI
#1: Protein | Mass: 23926.010 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4, KLNB1, hCG_1641510 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C4DFQ5 |
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#2: Protein | Mass: 18140.520 Da / Num. of mol.: 1 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, 635 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #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: 3.24 Å3/Da / Density % sol: 62.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.4M Ammonium Sulfate, 2%PEG400, 10mM CdCl2 |
-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 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→50 Å / Num. obs: 120718 / % possible obs: 96.8 % / Redundancy: 5 % / Rsym value: 0.073 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.33→1.35 Å / Redundancy: 2.6 % / Num. unique obs: 4059 / Rsym value: 0.798 / % possible all: 65.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4k8y, 6DWF Resolution: 1.33→39 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.421 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.035 / 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: 128.01 Å2 / Biso mean: 18.849 Å2 / Biso min: 5.54 Å2
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Refinement step | Cycle: final / Resolution: 1.33→39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.334→1.369 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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