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Yorodumi- PDB-3aue: A simplified BPTI variant with poly His amino acid tag (C5H) at t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aue | ||||||
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Title | A simplified BPTI variant with poly His amino acid tag (C5H) at the C-terminus | ||||||
Components | Bovine pancreatic trypsin inhibitorAprotinin | ||||||
Keywords | HYDROLASE INHIBITOR / Serine protease inhibitor / Inhibits serine protease / Trypsin | ||||||
Function / homology | Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Few Secondary Structures / Irregular Function and homology information | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Islam, M.M. / Kato, A. / Khan, M.M.A. / Noguchi, K. / Yohda, M. / Kidokoro, S.I. / Kuroda, Y. | ||||||
Citation | Journal: To be Published Title: Effect of amino acid mutations on protein's solubility, function and structure characterized using short poly amino acid peptide tags Authors: Islam, M.M. / Kato, A. / Khan, M.M.A. / Noguchi, K. / Yohda, M. / Kidokoro, S.I. / Kuroda, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aue.cif.gz | 190.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aue.ent.gz | 154 KB | Display | PDB format |
PDBx/mmJSON format | 3aue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/3aue ftp://data.pdbj.org/pub/pdb/validation_reports/au/3aue | HTTPS FTP |
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-Related structure data
Related structure data | 3aucC 3audC 3auhC 3auiC 4ptiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 6791.661 Da / Num. of mol.: 8 / Mutation: A1014G, A1038V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cell line (production host): JM109(DE3)PLYSS / Cellular location (production host): Inclusion body / Production host: Escherichia Coli (E. coli) #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Sequence details | THIS SEQUENCE IS A SIMPLIFIED BPTI VARIANT WITH 21 ALANINES, AND IT HAS BEEN STABILIZED WITH THE ...THIS SEQUENCE IS A SIMPLIFIED | |
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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: 2.21 Å3/Da / Density % sol: 44.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG4000, 0.2M Lithium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 30, 2009 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.28→38.954 Å / Num. all: 21392 / Num. obs: 21392 / % possible obs: 77.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 1.7 % / Rmerge(I) obs: 0.225 |
Reflection shell | Resolution: 2.28→2.38 Å / % possible all: 77.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PTI Resolution: 2.28→38.95 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.909 / SU B: 16.56 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 19.941 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→38.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.284→2.38 Å / Total num. of bins used: 20
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