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- PDB-3ifk: Crystal Structure Of Calcium-Saturated Calmodulin N-terminal Doma... -

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Basic information

Entry
Database: PDB / ID: 3ifk
TitleCrystal Structure Of Calcium-Saturated Calmodulin N-terminal Domain Fragment, Residues 1-90
ComponentsCALMODULIN
KeywordsMETAL BINDING PROTEIN / CALMODULIN / EF HAND MOTIF / N-TERMINAL DOMAIN / N-DOMAIN / RESIDUES 1-90 / METHYLATION / PHOSPHORYLATION / Isopeptide bond / Phosphoprotein
Function / homology
Function and homology information


regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane ...regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / mitochondrion-endoplasmic reticulum membrane tethering / regulation of cardiac muscle cell action potential / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / protein phosphatase activator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / calcium channel regulator activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / phosphatidylinositol 3-kinase binding / enzyme regulator activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / potassium ion transmembrane transport / voltage-gated potassium channel complex / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / sperm midpiece / calcium channel complex / activation of adenylate cyclase activity / response to amphetamine / adenylate cyclase activator activity / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / calcium-mediated signaling / positive regulation of nitric-oxide synthase activity / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / cellular response to type II interferon / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / disordered domain specific binding / myelin sheath / growth cone / vesicle / transmembrane transporter binding / protein autophosphorylation / neuron projection / positive regulation of apoptotic process / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsWitt, T.J. / Newman, R.A. / Shea, M.A.
CitationJournal: Methods Enzymol. / Year: 2009
Title: Thermodynamics and conformational change governing domain-domain interactions of calmodulin.
Authors: O'Donnell, S.E. / Newman, R.A. / Witt, T.J. / Hultman, R. / Froehlig, J.R. / Christensen, A.P. / Shea, M.A.
History
DepositionJul 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4896
Polymers20,3282
Non-polymers1604
Water1,02757
1
A: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2443
Polymers10,1641
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2443
Polymers10,1641
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.285, 58.851, 67.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CALMODULIN / / CAM


Mass: 10164.141 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN FRAGMENT, RESIDUES 1-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat)
Gene: Calm1, Calm, Cam, Cam1, Calm2, Cam2, Camb, Calm3, Cam3, Camc
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): LYS-S / References: UniProt: P62161, UniProt: P0DP29*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG8000, 5mM calcium-chloride, 100mM citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 16, 2005
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→67.12 Å / Num. all: 16668 / Num. obs: 16668 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.03→2.08 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
JDirectordata collection
AMoREphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→67.12 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.887 / SU B: 4.991 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29314 740 5 %RANDOM
Rwork0.2372 ---
obs0.2401 13953 99.9 %-
all-13983 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.118 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.64 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.03→67.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 4 57 1429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221382
X-RAY DIFFRACTIONr_angle_refined_deg2.3721.9721854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88826.84276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.29515264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.151156
X-RAY DIFFRACTIONr_chiral_restr0.2140.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021050
X-RAY DIFFRACTIONr_nbd_refined0.3110.21121
X-RAY DIFFRACTIONr_nbtor_refined0.3540.21040
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2154
X-RAY DIFFRACTIONr_metal_ion_refined0.1670.222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3470.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.22
X-RAY DIFFRACTIONr_mcbond_it1.471.5877
X-RAY DIFFRACTIONr_mcangle_it2.19321382
X-RAY DIFFRACTIONr_scbond_it3.8813539
X-RAY DIFFRACTIONr_scangle_it6.0434.5472
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 55 -
Rwork0.254 976 -
obs--99.9 %

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