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Yorodumi- PDB-4yta: BOND LENGTH ANALYSIS OF ASP, GLU AND HIS RESIDUES IN TRYPSIN AT 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yta | |||||||||
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Title | BOND LENGTH ANALYSIS OF ASP, GLU AND HIS RESIDUES IN TRYPSIN AT 1.2A RESOLUTION | |||||||||
Components | Cationic trypsin | |||||||||
Keywords | HYDROLASE / SERINE PROTEASE | |||||||||
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: 1.2 Å | |||||||||
Authors | Fisher, S.J. / Helliwell, J.R. / Blakeley, M.P. / Cianci, M. / McSweeny, S. | |||||||||
Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012 Title: Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness. Authors: Fisher, S.J. / Blakeley, M.P. / Cianci, M. / McSweeney, S. / Helliwell, J.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yta.cif.gz | 187.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yta.ent.gz | 146.5 KB | Display | PDB format |
PDBx/mmJSON format | 4yta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/4yta ftp://data.pdbj.org/pub/pdb/validation_reports/yt/4yta | HTTPS FTP |
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-Related structure data
Related structure data | 3unxC 1n6xS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: PEPTIDASE S1 (UNP RESIDUES 24-246) / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
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-Non-polymers , 5 types, 351 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-BEN / | #6: Water | ChemComp-HOH / | |
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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: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 25% PEG8000, 0.2 M AMMONIUM SULFATE, 0.1 M TRIS-HCL, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 298K PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 9, 2009 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→33.45 Å / Num. obs: 65730 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 4.5 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N6X Resolution: 1.2→33.45 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 8.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.63 Å2 / ksol: 0.49 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.2→33.45 Å
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Refine LS restraints |
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LS refinement shell |
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