+Open data
-Basic information
Entry | Database: PDB / ID: 2yvi | ||||||
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Title | Crystal structure of a death domain of human ankryn protein | ||||||
Components | Ankyrin-1 | ||||||
Keywords | CELL ADHESION / homo sapiens / death domain / monomer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information spectrin-associated cytoskeleton / positive regulation of organelle organization / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / Neurofascin interactions / ankyrin-1 complex / CHL1 interactions / cytoskeletal anchor activity / M band / Interaction between L1 and Ankyrins ...spectrin-associated cytoskeleton / positive regulation of organelle organization / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / Neurofascin interactions / ankyrin-1 complex / CHL1 interactions / cytoskeletal anchor activity / M band / Interaction between L1 and Ankyrins / spectrin binding / exocytosis / axolemma / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / cytoskeleton organization / sarcoplasmic reticulum / protein localization to plasma membrane / sarcolemma / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / Z disc / ATPase binding / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / transmembrane transporter binding / cytoskeleton / neuron projection / structural molecule activity / enzyme binding / signal transduction / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å | ||||||
Authors | Ihsanawati / Bessho, Y. / Chen, L. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a death domain of human ankryn protein Authors: Ihsanawati / Bessho, Y. / Chen, L. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yvi.cif.gz | 32.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yvi.ent.gz | 21.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/2yvi ftp://data.pdbj.org/pub/pdb/validation_reports/yv/2yvi | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12208.591 Da / Num. of mol.: 1 / Fragment: UNP residues 1394-1497, death domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell Free system / Gene: ANK1, ANK / Plasmid: PK060123-20 / References: UniProt: P16157 |
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#2: Chemical | ChemComp-GOL / |
#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: 1.87 Å3/Da / Density % sol: 34.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M NaCl, 0.1M TrisCl pH8.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9782 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2006 |
Radiation | Monochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9782 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→30 Å / Num. obs: 7800 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 30.4 % / Biso Wilson estimate: 16.5 Å2 / Rsym value: 0.087 |
Reflection shell | Resolution: 1.92→1.99 Å / Rmerge(I) obs: 0.187 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.92→26.99 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 4857158.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.9707 Å2 / ksol: 0.383766 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 22.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.92→26.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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Xplor file |
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