+Open data
-Basic information
Entry | Database: PDB / ID: 3pz7 | ||||||
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Title | Crystal structure of Ccd1-DIX domain | ||||||
Components | Dixin | ||||||
Keywords | SIGNALING PROTEIN / DIX domain / oligomerization | ||||||
Function / homology | Function and homology information forebrain ventricular zone progenitor cell division / cerebral cortex radially oriented cell migration / gamma-tubulin binding / positive regulation of Wnt signaling pathway / negative regulation of neuron differentiation / canonical Wnt signaling pathway / regulation of microtubule cytoskeleton organization / regulation of actin cytoskeleton organization / actin binding / cytoskeleton ...forebrain ventricular zone progenitor cell division / cerebral cortex radially oriented cell migration / gamma-tubulin binding / positive regulation of Wnt signaling pathway / negative regulation of neuron differentiation / canonical Wnt signaling pathway / regulation of microtubule cytoskeleton organization / regulation of actin cytoskeleton organization / actin binding / cytoskeleton / protein domain specific binding / focal adhesion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.441 Å | ||||||
Authors | Liu, Y.T. / Wang, J.W. / Chen, L. / Wu, J.W. | ||||||
Citation | Journal: To be Published Title: Molecular basis of WNT Activation via the DIX-domain protein CCD1 Authors: Liu, Y.T. / Dan, Q.J. / Wang, J.W. / Feng, Y.G. / Chen, L. / Liang, J. / Li, Q.X. / Lin, S.C. / Wang, Z.X. / Wu, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pz7.cif.gz | 27 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pz7.ent.gz | 20.5 KB | Display | PDB format |
PDBx/mmJSON format | 3pz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/3pz7 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/3pz7 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 10632.595 Da / Num. of mol.: 1 / Fragment: DIX domain / Mutation: L436M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q155Q3 |
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#2: Chemical | ChemComp-EDO / |
#3: Water | ChemComp-HOH / |
Sequence details | THIS SEQUENCE IS ISOFORM 2, Q155Q3-2 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.46 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Sodium Cacodylate, 20% PEG 3350, 4% Ethylene Glycol, 0.2M Ammonium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU |
Detector | Detector: CCD / Date: Dec 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.44→31.581 Å / Num. all: 3680 / Num. obs: 3659 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 42.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.44→2.53 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.6 / Num. unique all: 346 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.441→31.581 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7468 / SU ML: 0.34 / σ(F): 1.91 / Phase error: 28.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.089 Å2 / ksol: 0.365 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 81.87 Å2 / Biso mean: 39.3058 Å2 / Biso min: 24.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.441→31.581 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.441→2.53 Å
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