+Open data
-Basic information
Entry | Database: PDB / ID: 5mny | |||||||||
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Title | Neutron structure of cationic trypsin in complex with aniline | |||||||||
Components | Cationic trypsin | |||||||||
Keywords | HYDROLASE / hydrogen bonding / protonation / protein-ligand interaction | |||||||||
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 | NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | |||||||||
Authors | Schiebel, J. / Schrader, T.E. / Ostermann, A. / Heine, A. / Klebe, G. | |||||||||
Funding support | 1items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: Charges Shift Protonation: Neutron Diffraction Reveals that Aniline and 2-Aminopyridine Become Protonated Upon Binding to Trypsin. Authors: Schiebel, J. / Gaspari, R. / Sandner, A. / Ngo, K. / Gerber, H.D. / Cavalli, A. / Ostermann, 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 | 5mny.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mny.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 5mny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mny_validation.pdf.gz | 343.8 KB | Display | wwPDB validaton report |
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Full document | 5mny_full_validation.pdf.gz | 343.8 KB | Display | |
Data in XML | 5mny_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 5mny_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/5mny ftp://data.pdbj.org/pub/pdb/validation_reports/mn/5mny | HTTPS FTP |
-Related structure data
Related structure data | 5mn1C 5mnaC 5mnbC 5mncC 5mnxC 5monC 5mooC 4i8hS 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
#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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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-WOT / |
#4: Chemical | ChemComp-DOD / |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 16.5% (w/v) PEG 8000 |
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 2.667 Å |
Detector | Type: MAATEL BIODIFF / Detector: IMAGE PLATE / Date: Jul 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron |
Radiation wavelength | Wavelength: 2.667 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→50 Å / Num. obs: 38342 / % possible obs: 93.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.253 |
Reflection shell | Resolution: 1.43→1.45 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.858 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I8H Resolution: 1.43→22.09 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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