+Open data
-Basic information
Entry | Database: PDB / ID: 3so8 | ||||||
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Title | Crystal Structure of ANKRA | ||||||
Components | Ankyrin repeat family A protein 2 | ||||||
Keywords | PROTEIN BINDING / Structural Genomics / Structural Genomics Consortium / SGC / ANK | ||||||
Function / homology | Function and homology information low-density lipoprotein particle receptor binding / regulation of protein-containing complex assembly / histone deacetylase binding / regulation of gene expression / cytoskeleton / ubiquitin protein ligase binding / protein kinase binding / protein-containing complex / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.9 Å | ||||||
Authors | Xu, C. / Bochkarev, A. / Bian, C.B. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Sci.Signal. / Year: 2012 Title: Sequence-Specific Recognition of a PxLPxI/L Motif by an Ankyrin Repeat Tumbler Lock. Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / ...Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / Pawson, T. / Yang, X.J. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3so8.cif.gz | 42.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3so8.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 3so8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3so8_validation.pdf.gz | 418.2 KB | Display | wwPDB validaton report |
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Full document | 3so8_full_validation.pdf.gz | 418.8 KB | Display | |
Data in XML | 3so8_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 3so8_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/3so8 ftp://data.pdbj.org/pub/pdb/validation_reports/so/3so8 | HTTPS FTP |
-Related structure data
Related structure data | 3uxgC 3uzdC 3v2oC 3v2xC 3v30C 3v31C 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: 17671.969 Da / Num. of mol.: 1 / Fragment: UNP residues 149-310 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANKRA2, ANKRA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H9E1 |
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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: 2.24 Å3/Da / Density % sol: 45.01 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Peg 3350, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 4, 2010 / Details: si |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 13040 / Num. obs: 13040 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→49.53 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.686 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.158 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.097 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→49.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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