+Open data
-Basic information
Entry | Database: PDB / ID: 2agg | |||||||||
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Title | succinyl-AAPK-trypsin acyl-enzyme at 1.28 A resolution | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / ACYL-ENZYME / SERINE PROTEASE / PROTEINASE / PEPTIDASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
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) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | |||||||||
Authors | Radisky, E.S. / Lee, J.M. / Lu, C.J. / Koshland Jr., D.E. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: Insights into the serine protease mechanism from atomic resolution structures of trypsin reaction intermediates Authors: Radisky, E.S. / Lee, J.M. / Lu, C.J. / Koshland Jr., D.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2agg.cif.gz | 115.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2agg.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 2agg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/2agg ftp://data.pdbj.org/pub/pdb/validation_reports/ag/2agg | HTTPS FTP |
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-Related structure data
Related structure data | 2ageSC 2agiC 2ah4C 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) / Organ: pancreas / References: UniProt: P00760, trypsin |
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#2: Protein/peptide | Mass: 471.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Compound details | THE P-NITROANALINE GROUP IN THE ORIGINAL LIGAND WAS LOST AS IT MADE THE ACYL_ENZYME COMPLEX. THE ...THE P-NITROANALI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium sulfate, bis-tris propane, calcium chloride, benzamidine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 26, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→46.63 Å / Num. all: 59870 / Num. obs: 59870 / % possible obs: 96.27 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.28→1.35 Å / % possible obs: 51.9 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.7 / Num. measured obs: 5122 / Rsym value: 0.475 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2AGE with ligand and solvent removed Resolution: 1.28→46.63 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.217 / SU ML: 0.023 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.041 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.963 Å2
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Refinement step | Cycle: LAST / Resolution: 1.28→46.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.28→1.313 Å / Total num. of bins used: 20
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