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Yorodumi- PDB-4tpy: High throughput screening using acoustic droplet ejection to comb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tpy | ||||||||||||
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Title | High throughput screening using acoustic droplet ejection to combine protein crystals and chemical libraries on crystallization plates at high density | ||||||||||||
Components | Cationic trypsin | ||||||||||||
Keywords | HYDROLASE / Thrombin / Serpins / Fibrin | ||||||||||||
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 / Resolution: 1.3 Å | ||||||||||||
Authors | Teplitsky, E. / Joshi, K. / Mullen, J.D. / Soares, A.S. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Struct.Biol. / Year: 2015 Title: High throughput screening using acoustic droplet ejection to combine protein crystals and chemical libraries on crystallization plates at high density. Authors: Teplitsky, E. / Joshi, K. / Ericson, D.L. / Scalia, A. / Mullen, J.D. / Sweet, R.M. / Soares, A.S. #1: Journal: Acta Crystallographica Section D Biological Crystallography Year: 2014 Title: Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes Authors: Yin, X. / Scalia, A. / Leroy, L. / Cuttitta, C.M. / Polizzo, G.M. / Ericson, D.L. / Roessler, C.G. / Campos, O. / Ma, M.Y. / Agarwal, R. / Jackimowicz, R. / Allaire, M. / Orville, A.M. / ...Authors: Yin, X. / Scalia, A. / Leroy, L. / Cuttitta, C.M. / Polizzo, G.M. / Ericson, D.L. / Roessler, C.G. / Campos, O. / Ma, M.Y. / Agarwal, R. / Jackimowicz, R. / Allaire, M. / Orville, A.M. / Sweet, R.M. / Soares, A.S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tpy.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tpy.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 4tpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/4tpy ftp://data.pdbj.org/pub/pdb/validation_reports/tp/4tpy | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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 Details: Bromine derivative identified using acoustic droplet ejection to screen 1728 distinct conditions on each micro plate. Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
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-Non-polymers , 7 types, 427 molecules
#2: Chemical | ChemComp-CA / | ||||||||||
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#3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-BR / #5: Chemical | ChemComp-BEN / | #6: Chemical | ChemComp-TRS / | #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7 Details: 30mg/ml trypsin and 10mg/ml benzamidine in buffer (10mM CaCl2, 20mM HEPES pH 7.0) is combined with 1x precipitant (20% PEG 8000, 20mM ammonium s., 100 mM Bis Tris pH 7.0). Vapour diffusion ...Details: 30mg/ml trypsin and 10mg/ml benzamidine in buffer (10mM CaCl2, 20mM HEPES pH 7.0) is combined with 1x precipitant (20% PEG 8000, 20mM ammonium s., 100 mM Bis Tris pH 7.0). Vapour diffusion against 2x precipitant (40% PEG 8000, 40mM ammonium s., 200mM Bis Tris pH 7.0). PH range: 7.0-7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9198 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 44900 / Num. obs: 44900 / % possible obs: 90.39 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 27.41 |
Reflection shell | Resolution: 1.3→1.32 Å / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 1.07 / % possible all: 33.2 |
-Processing
Software | Name: REFMAC / Version: 5.8.0069 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.3→43.95 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.837 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.323 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→43.95 Å
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