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Yorodumi- PDB-3if7: Structure of Calmodulin complexed with its first endogenous inhib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3if7 | ||||||
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Title | Structure of Calmodulin complexed with its first endogenous inhibitor, sphingosylphosphorylcholine | ||||||
Components | Calmodulin | ||||||
Keywords | CALCIUM BINDING PROTEIN / EF-hand / phospholipid / Isopeptide bond / Methylation / Phosphoprotein | ||||||
Function / homology | Function and homology information positive regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / spindle pole / protein domain specific binding / calcium ion binding / protein-containing complex / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kovacs, E. / Harmat, V. / Toth, J. / Vertessy, B.G. / Modos, K. / Kardos, J. / Liliom, K. | ||||||
Citation | Journal: Faseb J. / Year: 2010 Title: Structure and mechanism of calmodulin binding to a signaling sphingolipid reveal new aspects of lipid-protein interactions Authors: Kovacs, E. / Harmat, V. / Toth, J. / Vertessy, B.G. / Modos, K. / Kardos, J. / Liliom, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3if7.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3if7.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 3if7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3if7_validation.pdf.gz | 1004.7 KB | Display | wwPDB validaton report |
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Full document | 3if7_full_validation.pdf.gz | 1001.1 KB | Display | |
Data in XML | 3if7_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 3if7_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/3if7 ftp://data.pdbj.org/pub/pdb/validation_reports/if/3if7 | HTTPS FTP |
-Related structure data
Related structure data | 1linS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16721.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: brain / References: UniProt: P62157 | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SPU / #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: 2.31 Å3/Da / Density % sol: 46.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 50mM sodium cacodylate, 10mM CaCl2, 10mM MgCl2, 28% PEG 8000: Mixed with 10mM lipid in methanol solution and 1mM protein solution, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 21596 / Num. obs: 21596 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3047 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: N- and C-terminal domains of PDB entry 1LIN Resolution: 1.6→29.39 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.38 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.096 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.758 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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