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Yorodumi- PDB-5mo0: Neutron structure of cationic trypsin in complex with benzamidine -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mo0 | |||||||||
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Title | Neutron structure of cationic trypsin in complex with benzamidine | |||||||||
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: 1.502 Å | |||||||||
Authors | Schiebel, J. / Schrader, T.E. / Ostermann, A. / Heine, A. / Klebe, G. | |||||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes. Authors: Schiebel, J. / Gaspari, R. / Wulsdorf, T. / Ngo, K. / Sohn, C. / Schrader, T.E. / 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 | 5mo0.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mo0.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mo0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/5mo0 ftp://data.pdbj.org/pub/pdb/validation_reports/mo/5mo0 | HTTPS FTP |
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-Related structure data
Related structure data | 5mneC 5mnfC 5mngC 5mnhC 5mnnC 5mnoC 5mnqC 5mnzC 5mo2C 5mopC 5moqC 5mosC 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-BEN / |
#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, 13% (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: 2.673 Å |
Detector | Type: MAATEL BIODIFF / Detector: IMAGE PLATE / Date: Sep 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron |
Radiation wavelength | Wavelength: 2.673 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 31713 / % possible obs: 89.4 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.197 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 3.244 / % possible all: 69.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I8H Resolution: 1.502→25.433 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.96
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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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