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Yorodumi- PDB-5mnh: Cationic trypsin in complex with benzamidine (deuterated sample a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mnh | |||||||||
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Title | Cationic trypsin in complex with benzamidine (deuterated sample at 295 K) | |||||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 Å | |||||||||
Authors | Schiebel, J. / 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 | 5mnh.cif.gz | 129.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mnh.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 5mnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/5mnh ftp://data.pdbj.org/pub/pdb/validation_reports/mn/5mnh | HTTPS FTP |
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-Related structure data
Related structure data | 5mneC 5mnfC 5mngC 5mnnC 5mnoC 5mnqC 5mnzC 5mo0C 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 | #4: Chemical | ChemComp-BEN / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.25 % |
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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 |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.7749 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 0.93→42.618 Å / Num. obs: 145727 / % possible obs: 99.5 % / Redundancy: 8.633 % / Rsym value: 0.039 / Net I/σ(I): 28.68 |
Reflection shell | Resolution: 0.93→0.99 Å / Redundancy: 8.435 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 4.47 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I8H Resolution: 0.93→27.451 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 6.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.93→27.451 Å
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Refine LS restraints |
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LS refinement shell |
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