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- PDB-4u8d: X-ray structure of Mg-bound human sorcin -

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Basic information

Entry
Database: PDB / ID: 4u8d
TitleX-ray structure of Mg-bound human sorcin
ComponentsSorcin
Keywordscalcium binding protein / PENTA EF-HAND / multidrug resistance related protein
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 / muscle organ development / Reduction of cytosolic Ca++ levels / action potential ...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 / muscle organ development / Reduction of cytosolic Ca++ levels / action potential / regulation of heart contraction / 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 / calcium channel regulator activity / negative regulation of ryanodine-sensitive calcium-release channel activity / intracellular sequestering of iron ion / 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 / identical protein binding / membrane / cytoplasm / cytosol
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFiorillo, A. / Ilari, A. / Colotti, G.
CitationJournal: To be published
Title: INVESTIGATING THE CONFORMATIONAL CHANGES of SORCIN TO SHED LIGHT ON SIGNAL TRANSDUCTION IN THE APOPTOTIC PROCESS
Authors: Ilari, A. / Fiorillo, A. / Colotti, G.
History
DepositionAug 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorcin
B: Sorcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5619
Polymers43,3912
Non-polymers1707
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-67 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.832, 117.832, 86.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 3 / Auth seq-ID: 161 - 198 / Label seq-ID: 161 - 198

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsbiological unit is the same as asym.

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Components

#1: Protein Sorcin / 22 kDa protein / CP-22 / CP22 / V19


Mass: 21695.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30626
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.48 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000 10%, Mg(OAc)2 0.2M, cacodylate 0.1M pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 10, 2013
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.76 Å / Num. obs: 27800 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 36.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.029 / Net I/σ(I): 24 / Num. measured all: 356554 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.3812.10.9382.93201826520.880.27898.9
8.91-48.7611.40.0296.1650256910.00699.5

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Processing

Software
NameVersionClassification
XDSJanuary 10, 2014data reduction
Aimless0.2.8data scaling
PDB_EXTRACT3.14data extraction
REFMAC5.8.0073refinement
MOLREPphasing
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UPG

4upg


Resolution: 2.3→48.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2486 / WRfactor Rwork: 0.1973 / FOM work R set: 0.787 / SU B: 6.049 / SU ML: 0.142 / SU R Cruickshank DPI: 0.2047 / SU Rfree: 0.193 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 1390 5 %RANDOM
Rwork0.1973 26313 --
obs0.1998 27703 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.97 Å2 / Biso mean: 43.793 Å2 / Biso min: 24.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20 Å2
2---1.5 Å20 Å2
3---3 Å2
Refinement stepCycle: final / Resolution: 2.3→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 7 166 2877
Biso mean--55.57 46.98 -
Num. residues----344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022795
X-RAY DIFFRACTIONr_bond_other_d0.0020.022561
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9453759
X-RAY DIFFRACTIONr_angle_other_deg0.84735868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3145348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49624.126143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43815462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1041522
X-RAY DIFFRACTIONr_chiral_restr0.0870.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023251
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02691
X-RAY DIFFRACTIONr_mcbond_it2.9784.2111380
X-RAY DIFFRACTIONr_mcbond_other2.9754.211379
X-RAY DIFFRACTIONr_mcangle_it4.6776.3051723
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
367LOOSE POSITIONAL1.095
226TIGHT THERMAL1.890.5
367LOOSE THERMAL4.910
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 99 -
Rwork0.236 1904 -
all-2003 -
obs--98.23 %

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