+Open data
-Basic information
Entry | Database: PDB / ID: 6zq2 | ||||||
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Title | Cationic trypsin in complex with a derivative of benzamidine | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE / digestive enzyme / digestion / TRYPSIN INHIBITOR / BENZAMIDINE / cationic trypsin / bovine trypsin | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Sandner, A. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To be published Title: Cationic trypsin in complex with a derivative of benzamidine Authors: Sandner, A. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zq2.cif.gz | 163.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zq2.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zq2_validation.pdf.gz | 383.5 KB | Display | wwPDB validaton report |
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Full document | 6zq2_full_validation.pdf.gz | 384 KB | Display | |
Data in XML | 6zq2_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 6zq2_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/6zq2 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/6zq2 | HTTPS FTP |
-Related structure data
Related structure data | 5mnkS S: Starting model for refinement |
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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 , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
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-Non-polymers , 5 types, 224 molecules
#2: Chemical | ChemComp-32U / | ||||
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#3: Chemical | ChemComp-CA / | ||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.35 Å3/Da / Density % sol: 74.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1% (NH4)2SO4 0.1% imidazole 22% PEG 8000 0.1% NaN3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 27, 2020 / Details: Signally blended Si111 crystal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→47.5 Å / Num. obs: 48302 / % possible obs: 99.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 12.96 Å2 / CC1/2: 1 / Rsym value: 0.05 / Net I/σ(I): 26.12 |
Reflection shell | Resolution: 1.29→1.37 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 3.68 / Num. unique obs: 7699 / CC1/2: 0.93 / Rsym value: 0.54 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MNK Resolution: 1.29→23.73 Å / SU ML: 0.0904 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.3645 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→23.73 Å
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Refine LS restraints |
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LS refinement shell |
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