+Open data
-Basic information
Entry | Database: PDB / ID: 4lg6 | ||||||
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Title | Crystal structure of ANKRA2-CCDC8 complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Structural Genomics Consortium / SGC / ankyrin repeat | ||||||
Function / homology | Function and homology information 3M complex / negative regulation of phosphatase activity / regulation of mitotic nuclear division / low-density lipoprotein particle receptor binding / regulation of protein-containing complex assembly / post-translational protein modification / microtubule cytoskeleton organization / histone deacetylase binding / Neddylation / regulation of gene expression ...3M complex / negative regulation of phosphatase activity / regulation of mitotic nuclear division / low-density lipoprotein particle receptor binding / regulation of protein-containing complex assembly / post-translational protein modification / microtubule cytoskeleton organization / histone deacetylase binding / Neddylation / regulation of gene expression / cytoskeleton / centrosome / ubiquitin protein ligase binding / protein kinase binding / protein-containing complex / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Xu, C. / Bian, C. / Tempel, W. / Mackenzie, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Structure / Year: 2015 Title: Ankyrin Repeats of ANKRA2 Recognize a PxLPxL Motif on the 3M Syndrome Protein CCDC8. Authors: Nie, J. / Xu, C. / Jin, J. / Aka, J.A. / Tempel, W. / Nguyen, V. / You, L. / Weist, R. / Min, J. / Pawson, T. / Yang, X.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lg6.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lg6.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 4lg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/4lg6 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/4lg6 | HTTPS FTP |
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-Related structure data
Related structure data | 3so8S S: Starting model for refinement |
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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: 18784.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANKRA2, ANKRA / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9H9E1 | ||
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#2: Protein/peptide | Mass: 2077.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H0W5 | ||
#3: Chemical | #4: 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 Å3/Da / Density % sol: 39.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, pH 7.5, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 9, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→40.818 Å / Num. all: 14082 / Num. obs: 14082 / % possible obs: 97 % / Redundancy: 3.7 % / Rsym value: 0.047 / Net I/σ(I): 16.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SO8 Resolution: 1.8→26.149 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.465 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE program coot and the molprobity server were also used during refinement.
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.83 Å2 / Biso mean: 29.629 Å2 / Biso min: 13.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→26.149 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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