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- PDB-4usl: The X-ray structure of calcium bound human sorcin -

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Basic information

Entry
Database: PDB / ID: 4usl
TitleThe X-ray structure of calcium bound human sorcin
Components(SORCINSRI (gene)) x 2
KeywordsMETAL BINDING PROTEIN / PENTA EF-HANDS CALCIUM BINDING PROTEIN / ENDOPLASMIC RETICULUM STRESS
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
EF-hand domain / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...EF-hand domain / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Sorcin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsIlari, A. / Fiorillo, A. / Colotti, G.
CitationJournal: 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
DepositionJul 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SORCIN
D: SORCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1208
Polymers24,6922
Non-polymers4296
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-51.3 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.369, 111.580, 60.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2027-

HOH

21A-2042-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

#1: Protein SORCIN / SRI (gene) / 22 KDA PROTEIN / CP-22 / CP22 / V19 / SOLUBLE RESISTANCE RELATED


Mass: 21695.336 Da / Num. of mol.: 1
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
#2: Protein/peptide SORCIN / SRI (gene) / 22 KDA PROTEIN / CP-22 / CP22 / V19


Mass: 2996.209 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-32
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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Non-polymers , 4 types, 130 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.18 % / Description: NONE
Crystal growpH: 8.5
Details: PEG 3350 25% W/V, LISO4 0.5 M, 0.1 M TRIS, PH=8.5, CACL2 0.005M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 20590 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 21.57
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JUO

1juo


Resolution: 1.65→37.34 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.248 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22135 1110 5.1 %RANDOM
Rwork0.19187 ---
obs0.19331 20590 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.993 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å20 Å20 Å2
2---0.86 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.65→37.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 22 124 1552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021496
X-RAY DIFFRACTIONr_bond_other_d0.0020.021376
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9522026
X-RAY DIFFRACTIONr_angle_other_deg0.83933165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9435191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69724.23178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98515245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.281511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021750
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02375
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 86 -
Rwork0.329 1494 -
obs--99.31 %

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