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Yorodumi- PDB-2o6n: RH4B: designed right-handed coiled coil tetramer with all biologi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o6n | ||||||
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Title | RH4B: designed right-handed coiled coil tetramer with all biological amino acids | ||||||
Components | RH4B designed peptide | ||||||
Keywords | DE NOVO PROTEIN / RIGHT-HANDED / TETRAMER | ||||||
Function / homology | YTTERBIUM (II) ION Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.1 Å | ||||||
Authors | Sales, M. / Alber, T. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Structure of a designed, right-handed coiled-coil tetramer containing all biological amino acids. Authors: Sales, M. / Plecs, J.J. / Holton, J.M. / Alber, T. | ||||||
History |
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Remark 999 | SEQUENCE The sequence was computationally designed to optimize the stability and specificity of a ...SEQUENCE The sequence was computationally designed to optimize the stability and specificity of a right-handed coiled- coil tetramer |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o6n.cif.gz | 46.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o6n.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 2o6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o6n_validation.pdf.gz | 414 KB | Display | wwPDB validaton report |
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Full document | 2o6n_full_validation.pdf.gz | 414 KB | Display | |
Data in XML | 2o6n_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 2o6n_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/2o6n ftp://data.pdbj.org/pub/pdb/validation_reports/o6/2o6n | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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Details | The biological assembly is the tetramer generated from the monomer in the asymmetric unit by the 4 operations: x,y,z; y-1/2,-x+1/2,z; -x,1-y,z; -y+1/2,x+1/2,z. |
-Components
#1: Protein/peptide | Mass: 3947.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical peptide synthesis |
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#2: Chemical | ChemComp-YB2 / |
#3: 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: 2.31 Å3/Da / Density % sol: 46.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 10% PEG 4000, 0.1M ammonium sulfate, 0.15M sodium acetate, 10mM ytterbium(II) chloride, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.000,1.2398,1.3858,1.3864 | |||||||||||||||
Detector | Detector: IMAGE PLATE / Date: Feb 28, 2000 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1→30.36 Å / Num. all: 20717 / Num. obs: 20631 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.074 / Net I/σ(I): 21.09 | |||||||||||||||
Reflection shell | Resolution: 1→1.05 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.011 / Mean I/σ(I) obs: 1.26 / Rsym value: 0.85 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.1→30.36 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.662 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.026 / ESU R Free: 0.025 / 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: 11.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→30.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.13 Å / Total num. of bins used: 20
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