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- PDB-3if7: Structure of Calmodulin complexed with its first endogenous inhib... -

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Basic information

Entry
Database: PDB / ID: 3if7
TitleStructure of Calmodulin complexed with its first endogenous inhibitor, sphingosylphosphorylcholine
ComponentsCalmodulin
KeywordsCALCIUM 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 / spindle pole / protein domain specific binding / calcium ion binding / protein-containing complex / cytosol / cytoplasm
Similarity search - Function
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
Chem-SPU / Calmodulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKovacs, E. / Harmat, V. / Toth, J. / Vertessy, B.G. / Modos, K. / Kardos, J. / Liliom, K.
CitationJournal: 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
DepositionJul 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7449
Polymers16,7211
Non-polymers2,0238
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.669, 39.669, 170.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-164-

HOH

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Components

#1: Protein Calmodulin / / CaM


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
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SPU / 2-{[(R)-{[(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium / sphingosylphosphorylcholine, sphingosine phosphorylcholine


Mass: 465.627 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H50N2O5P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N- and C-terminal domains of PDB entry 1LIN

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
RfactorNum. reflection% reflectionSelection details
Rfree0.23825 1103 5.1 %RANDOM
Rwork0.19232 ---
all0.19459 20426 --
obs0.19459 20426 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.758 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 84 79 1246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221187
X-RAY DIFFRACTIONr_bond_other_d0.0050.02809
X-RAY DIFFRACTIONr_angle_refined_deg2.0852.0221593
X-RAY DIFFRACTIONr_angle_other_deg1.11331987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3235146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96726.03458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87415199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.654156
X-RAY DIFFRACTIONr_chiral_restr0.1340.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
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_it1.7651.5707
X-RAY DIFFRACTIONr_mcbond_other0.5781.5295
X-RAY DIFFRACTIONr_mcangle_it2.96521128
X-RAY DIFFRACTIONr_scbond_it3.8973480
X-RAY DIFFRACTIONr_scangle_it6.4694.5462
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 76 -
Rwork0.2 1478 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.18510.13651.41530.0378-0.1372.84290.1095-0.0012-0.14780.0093-0.0073-0.00780.08720.1803-0.10210.02050.0187-0.01510.0444-0.00250.0202-35.746714.8822-10.9215
22.6177-0.2779-0.40561.7183-0.1351.4050.0075-0.06570.06880.07370.00770.16660.0217-0.1013-0.01520.0057-0.0030.00450.0126-0.00320.0284-20.541317.7005-22.184
30.3295-0.61951.4921.1767-2.69967.838-0.034-0.0389-0.1080.11220.11880.24360.0777-0.0167-0.08480.19540.03620.03710.26130.00510.2715-27.64514.4227-16.0693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 78
2X-RAY DIFFRACTION1A149 - 150
3X-RAY DIFFRACTION2A81 - 146
4X-RAY DIFFRACTION2A151 - 152
5X-RAY DIFFRACTION3A153 - 156

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