+Open data
-Basic information
Entry | Database: PDB / ID: 4db6 | ||||||
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Title | Designed Armadillo repeat protein (YIIIM3AII) | ||||||
Components | Armadillo repeat protein | ||||||
Keywords | DE NOVO PROTEIN / Solenoid repeat / Armadillo repeat motif | ||||||
Function / homology | Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Madhurantakam, C. / Varadamsetty, G. / Grutter, M.G. / Pluckthun, A. / Mittl, P.R.E. | ||||||
Citation | Journal: Protein Sci. / Year: 2012 Title: Structure-based optimization of designed Armadillo-repeat proteins. Authors: Madhurantakam, C. / Varadamsetty, G. / Grutter, M.G. / Pluckthun, A. / Mittl, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4db6.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4db6.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 4db6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/4db6 ftp://data.pdbj.org/pub/pdb/validation_reports/db/4db6 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 22482.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue |
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#2: 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: 2.03 Å3/Da / Density % sol: 39.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES,pH 7.5, 1.4 M sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.93 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2010 / Details: Mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→30 Å / Num. obs: 26356 / % possible obs: 98.7 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→22.895 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 20.34 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.783 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.5164 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→22.895 Å
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Refine LS restraints |
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LS refinement shell |
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