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- PDB-3v2q: COMPcc in complex with fatty acids -

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Basic information

Entry
Database: PDB / ID: 3v2q
TitleCOMPcc in complex with fatty acids
ComponentsCartilage Oligomerization matrix protein (coiled-coil domain)
KeywordsPROTEIN BINDING / coiled coil palmitic acid / storage
Function / homology
Function and homology information


cartilage homeostasis / tendon development / negative regulation of hemostasis / musculoskeletal movement / vascular associated smooth muscle contraction / ECM proteoglycans / vascular associated smooth muscle cell development / bone growth / chondrocyte development / BMP binding ...cartilage homeostasis / tendon development / negative regulation of hemostasis / musculoskeletal movement / vascular associated smooth muscle contraction / ECM proteoglycans / vascular associated smooth muscle cell development / bone growth / chondrocyte development / BMP binding / chondrocyte proliferation / endochondral bone growth / growth plate cartilage development / Integrin cell surface interactions / vitamin D binding / positive regulation of chondrocyte proliferation / muscle cell development / regulation of bone mineralization / heparan sulfate proteoglycan binding / collagen fibril organization / bone morphogenesis / cartilage development / limb development / proteoglycan binding / neuromuscular process / artery morphogenesis / skin development / extracellular matrix structural constituent / bone mineralization / fibronectin binding / response to unfolded protein / protein secretion / BMP signaling pathway / collagen binding / ossification / skeletal system development / protein homooligomerization / multicellular organism growth / protein processing / platelet aggregation / cellular senescence / blood coagulation / integrin binding / heparin binding / regulation of gene expression / collagen-containing extracellular matrix / protease binding / apoptotic process / calcium ion binding / negative regulation of apoptotic process / protein-containing complex / extracellular space / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #10 / : / Thrombospondin/cartilage oligomeric matrix protein, coiled-coil domain / Thrombospondin-5, coiled coil region / Cartilage oligomeric matrix protein / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #10 / : / Thrombospondin/cartilage oligomeric matrix protein, coiled-coil domain / Thrombospondin-5, coiled coil region / Cartilage oligomeric matrix protein / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / : / Calcium-binding EGF domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand calcium-binding domain. / Concanavalin A-like lectin/glucanase domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PALMITIC ACID / Cartilage oligomeric matrix protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStetefeld, J.
CitationJournal: Plos One / Year: 2012
Title: The pentameric channel of COMPcc in complex with different fatty acids.
Authors: MacFarlane, A.A. / Orriss, G. / Okun, N. / Meier, M. / Klonisch, T. / Khajehpour, M. / Stetefeld, J.
History
DepositionDec 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cartilage Oligomerization matrix protein (coiled-coil domain)
B: Cartilage Oligomerization matrix protein (coiled-coil domain)
C: Cartilage Oligomerization matrix protein (coiled-coil domain)
D: Cartilage Oligomerization matrix protein (coiled-coil domain)
E: Cartilage Oligomerization matrix protein (coiled-coil domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7237
Polymers26,2105
Non-polymers5132
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12190 Å2
ΔGint-114 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.696, 48.573, 53.318
Angle α, β, γ (deg.)90.00, 103.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Cartilage Oligomerization matrix protein (coiled-coil domain)


Mass: 5242.078 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: COMPcc / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R0G6*PLUS
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.86 Å3/Da / Density % sol: 33.74 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.25 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 2.2→14 Å / Num. all: 9799 / Num. obs: 228026 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 29.7 Å2

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Processing

Software
NameVersionClassificationNB
CNS1.3refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→14 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 771326 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1016 10.4 %RANDOM
Rwork0.209 ---
obs-9799 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 84.2949 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 106.82 Å2 / Biso mean: 50.4628 Å2 / Biso min: 27.46 Å2
Baniso -1Baniso -2Baniso -3
1-7.42 Å20 Å21.4 Å2
2---4.99 Å20 Å2
3----2.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 36 208 2054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d15.7
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 156 9.6 %
Rwork0.23 1476 -
all-1632 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6plm.parplm.top

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