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Open data
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Basic information
Entry | Database: PDB / ID: 2jc2 | ||||||
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Title | The crystal structure of the natural F112L human sorcin mutant | ||||||
![]() | SORCIN![]() | ||||||
![]() | METAL BINDING PROTEIN / RYANODINE RECEPTOR INTERACTING PROTEIN / ![]() ![]() | ||||||
Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Franceschini, S. / Ilari, A. / Colotti, G. / Chiancone, E. | ||||||
![]() | ![]() Title: Molecular Basis for the Impaired Function of the Natural F112L Sorcin Mutant: X-Ray Crystal Structure, Calcium Affinity, and Interaction with Annexin Vii and the Ryanodine Receptor. Authors: Franceschini, S. / Ilari, A. / Verzili, D. / Zamparelli, C. / Antaramian, A. / Rueda, A. / Valdivia, H.H. / Chiancone, E. / Colotti, G. #1: ![]() Title: The Crystal Structure of the Sorcin Calcium Binding Domain Provides a Model of Calcium-Dependent Processes in the Full Length Protein Authors: Ilari, A. / Johnson, K.A. / Nastopoulos, V. / Verzili, D. / Zamparelli, C. / Colotti, G. / Tsernoglou, D. / Chiancone, E. #2: ![]() Title: Crystal Structure of Calcium-Free Human Sorcin: A Member of the Penta-EF-Hand Protein Family Authors: Xie, X. / Dwyer, M.D. / Swenson, L. / Parker, M.H. / Botfield, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.4 KB | Display | ![]() |
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PDB format | ![]() | 111.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1juoS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 33 - 198 / Label seq-ID: 33 - 198
NCS ensembles :
NCS oper: (Code: given Matrix: (0.50028, 0.86586, -0.00026), Vector ![]() |
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Components
#1: Protein | ![]() Mass: 21661.320 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / ![]() #3: Water | ChemComp-HOH / | ![]() Compound details | ENGINEERED RESIDUE IN CHAIN A, PHE 112 TO LEU ENGINEERED RESIDUE IN CHAIN B, PHE 112 TO LEU ...ENGINEERED | Sequence details | F112L IS A NATURAL HUMAN SORCIN MUTANT. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.52 % / Description: NONE |
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Crystal grow![]() | pH: 5.7 / Details: AMMONIUM SULFATE 1.0M, PH 5.7, 12% V/V DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→50 Å / Num. obs: 25105 / % possible obs: 96.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / % possible all: 85.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1JUO Resolution: 2.5→45.5 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.887 / SU B: 12.596 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 1.059 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM M1 TO Q32 ARE MISSING IN THE STRUCTURE BECAUSE OF AN INSUFFICIENT ELECTRON DENSITY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→45.5 Å
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Refine LS restraints |
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