+Open data
-Basic information
Entry | Database: PDB / ID: 8ygy | ||||||
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Title | Structure of the KLK1 from Biortus. | ||||||
Components | Kallikrein-1 | ||||||
Keywords | HYDROLASE / Protease / Serine protease | ||||||
Function / homology | Function and homology information tissue kallikrein / regulation of systemic arterial blood pressure / zymogen activation / secretory granule / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / serine-type endopeptidase activity / extracellular exosome / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å | ||||||
Authors | Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of the KLK1 from Biortus. Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ygy.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ygy.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ygy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ygy_validation.pdf.gz | 769 KB | Display | wwPDB validaton report |
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Full document | 8ygy_full_validation.pdf.gz | 769.5 KB | Display | |
Data in XML | 8ygy_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 8ygy_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/8ygy ftp://data.pdbj.org/pub/pdb/validation_reports/yg/8ygy | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26429.541 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLK1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06870, tissue kallikrein | ||||
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#2: Polysaccharide | alpha-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M (NH4)2SO4, 0.1M Bis-Tris pH6.5, 25% PEG3,350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18082 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18082 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.75 Å / Num. obs: 9127 / % possible obs: 88.1 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.981 / Num. unique obs: 513 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.401→45.75 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.33 / SU ML: 0.223 / Cross valid method: FREE R-VALUE / ESU R: 0.808 / ESU R Free: 0.301 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.974 Å2
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Refinement step | Cycle: LAST / Resolution: 2.401→45.75 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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