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- PDB-1qx5: Crystal structure of apoCalmodulin -

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Basic information

Entry
Database: PDB / ID: 1qx5
TitleCrystal structure of apoCalmodulin
ComponentsCalmodulin
KeywordsSIGNALING PROTEIN / apoCalmodulin / domain swap / dimer / EF hands / calcium binding protein
Function / homology
Function and homology information


regulation of store-operated calcium channel activity / : / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / : / : / : / : ...regulation of store-operated 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 / positive regulation of DNA binding / negative regulation of high voltage-gated calcium channel activity / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / catalytic complex / detection of calcium ion / regulation of synaptic vesicle endocytosis / regulation of cardiac muscle contraction / postsynaptic cytosol / activation of adenylate cyclase activity / cellular response to interferon-beta / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / presynaptic cytosol / positive regulation of nitric-oxide synthase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / titin binding / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / regulation of heart rate / calyx of Held / response to amphetamine / adenylate cyclase activator activity / sarcomere / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / calcium channel regulator activity / positive regulation of receptor signaling pathway via JAK-STAT / calcium-mediated signaling / response to calcium ion / cellular response to type II interferon / G2/M transition of mitotic cell cycle / Schaffer collateral - CA1 synapse / spindle pole / disordered domain specific binding / calcium-dependent protein binding / myelin sheath / protein autophosphorylation / growth cone / vesicle / transmembrane transporter binding / neuron projection / positive regulation of apoptotic process / protein domain specific binding / calcium ion binding / centrosome / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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 ...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
Calmodulin-1 / Calmodulin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.54 Å
AuthorsSchumacher, M.A. / Crum, M. / Miller, M.C.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal structures of apocalmodulin and an apocalmodulin/SK potassium channel gating domain complex.
Authors: Schumacher, M.A. / Crum, M. / Miller, M.C.
History
DepositionSep 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Calmodulin
I: Calmodulin
B: Calmodulin
J: Calmodulin
K: Calmodulin
T: Calmodulin
R: Calmodulin
Y: Calmodulin


Theoretical massNumber of molelcules
Total (without water)133,7718
Polymers133,7718
Non-polymers00
Water3,153175
1
D: Calmodulin
Y: Calmodulin


Theoretical massNumber of molelcules
Total (without water)33,4432
Polymers33,4432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-37 kcal/mol
Surface area14400 Å2
MethodPISA
2
I: Calmodulin
R: Calmodulin


Theoretical massNumber of molelcules
Total (without water)33,4432
Polymers33,4432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-38 kcal/mol
Surface area14510 Å2
MethodPISA
3
J: Calmodulin
T: Calmodulin


Theoretical massNumber of molelcules
Total (without water)33,4432
Polymers33,4432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-37 kcal/mol
Surface area14460 Å2
MethodPISA
4
B: Calmodulin
K: Calmodulin


Theoretical massNumber of molelcules
Total (without water)33,4432
Polymers33,4432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-38 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.000, 146.000, 78.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsapoCaM forms a domain swapped dimer: there are four, essentially identical dimers in the ASU

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Components

#1: Protein
Calmodulin


Mass: 16721.350 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Gene: CALM1, CAM1, CALM, CAM, CALM2, CAM2, CAMB, CALM3, CAM3, CAMC
Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62161, UniProt: P0DP29*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.59 Å3/Da / Density % sol: 65.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Citrate, 150 mM NaCl, Hepes , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.989 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 2.54→66.4 Å / Num. all: 61810 / Num. obs: 61810 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 75.4 Å2 / Rsym value: 0.047 / Net I/σ(I): 10.2
Reflection shellResolution: 2.54→2.7 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.54→66.39 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3041 5 %RANDOM
Rwork0.227 ---
all0.229 60402 --
obs0.227 60402 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.8149 Å2 / ksol: 0.374381 e/Å3
Displacement parametersBiso mean: 71.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å29.51 Å20 Å2
2---0.81 Å20 Å2
3---1.61 Å2
Refine analyzeLuzzati coordinate error free: 0.48 Å / Luzzati sigma a free: 0.51 Å
Refinement stepCycle: LAST / Resolution: 2.54→66.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9158 0 0 175 9333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.08
LS refinement shellResolution: 2.54→2.7 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.493 511 5.1 %
Rwork0.4 9531 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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