+Open data
-Basic information
Entry | Database: PDB / ID: 4upg | ||||||
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Title | X-ray structure of calcium-free human sorcin | ||||||
Components | SORCINSRI (gene) | ||||||
Keywords | METAL BINDING PROTEIN / CA-BINDING PROTEIN / PENTA-EF HAND / APOPTOSIS REGULATION | ||||||
Function / homology | Function and homology information regulation of relaxation of muscle / regulation of high voltage-gated calcium channel activity / regulation of cell communication by electrical coupling / regulation of striated muscle contraction / negative regulation of cardiac muscle contraction / regulation of cardiac muscle cell contraction / Sodium/Calcium exchangers / regulation of heart contraction / muscle organ development / Reduction of cytosolic Ca++ levels ...regulation of relaxation of muscle / regulation of high voltage-gated calcium channel activity / regulation of cell communication by electrical coupling / regulation of striated muscle contraction / negative regulation of cardiac muscle contraction / regulation of cardiac muscle cell contraction / Sodium/Calcium exchangers / regulation of heart contraction / muscle organ development / Reduction of cytosolic Ca++ levels / action potential / negative regulation of heart rate / regulation of cell communication by electrical coupling involved in cardiac conduction / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of calcium ion transport / Ion transport by P-type ATPases / intracellular sequestering of iron ion / calcium channel regulator activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / T-tubule / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / Stimuli-sensing channels / Z disc / calcium ion transport / heart development / DNA-binding transcription factor binding / protease binding / transmembrane transporter binding / protein heterodimerization activity / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / signal transduction / extracellular exosome / nucleoplasm / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Ilari, A. / Fiorillo, A. / Colotti, G. | ||||||
Citation | Journal: Sci.Rep. / Year: 2015 Title: Structural Basis of Sorcin-Mediated Calcium-Dependent Signal Transduction. Authors: Ilari, A. / Fiorillo, A. / Poser, E. / Lalioti, V.S. / Sundell, G.N. / Ivarsson, Y. / Genovese, I. / Colotti, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4upg.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4upg.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 4upg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/4upg ftp://data.pdbj.org/pub/pdb/validation_reports/up/4upg | HTTPS FTP |
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-Related structure data
Related structure data | 4uslC 1juoS S: Starting model for refinement 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19074.498 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30626 | ||||
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#2: Chemical | ChemComp-SO4 / #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: 2.58 Å3/Da / Density % sol: 43.9 % / Description: NONE |
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Crystal grow | Details: 20% PEG4000, 0.3 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 197835 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.82 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.61 / % possible all: 98.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JUO Resolution: 2.1→40.59 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.939 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.162 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.342 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40.59 Å
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