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- PDB-1mz9: Storage function of COMP:the crystal structure of the coiled-coil... -

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Basic information

Entry
Database: PDB / ID: 1mz9
TitleStorage function of COMP:the crystal structure of the coiled-coil domain in complex with vitamin D3
Componentscartilage oligomeric matrix protein
KeywordsPROTEIN BINDING / pentameric coiled-coil domain
Function / homology
Function and homology information


tendon development / negative regulation of hemostasis / cartilage homeostasis / musculoskeletal movement / vascular associated smooth muscle contraction / ECM proteoglycans / chondrocyte development / vascular associated smooth muscle cell development / bone growth / BMP binding ...tendon development / negative regulation of hemostasis / cartilage homeostasis / musculoskeletal movement / vascular associated smooth muscle contraction / ECM proteoglycans / chondrocyte development / vascular associated smooth muscle cell development / bone growth / 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 / bone morphogenesis / collagen fibril organization / cartilage development / limb development / proteoglycan binding / artery morphogenesis / extracellular matrix structural constituent / neuromuscular process / skin development / 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 / protease binding / collagen-containing extracellular matrix / calcium ion binding / negative regulation of apoptotic process / 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
Chem-VDY / Cartilage oligomeric matrix protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsStetefeld, J.
CitationJournal: EMBO J. / Year: 2002
Title: Storage function of cartilage oligomeric matrix protein: the crystal structure of the coiled-coil domain in complex with vitamin D(3).
Authors: Ozbek, S. / Engel, J. / Stetefeld, J.
History
DepositionOct 7, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cartilage oligomeric matrix protein
B: cartilage oligomeric matrix protein
C: cartilage oligomeric matrix protein
D: cartilage oligomeric matrix protein
E: cartilage oligomeric matrix protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0127
Polymers26,2105
Non-polymers8012
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13390 Å2
ΔGint-113 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.295, 49.289, 55.260
Angle α, β, γ (deg.)90.00, 103.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
cartilage oligomeric matrix protein


Mass: 5242.078 Da / Num. of mol.: 5 / Fragment: RESIDUES 27-71
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET3b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109-DE3 / References: UniProt: Q9R0G6
#2: Chemical ChemComp-VDY / 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL / 25-HYDROXYVITAMIN D3


Mass: 400.637 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H44O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.2 Msodium acetate1reservoir
30.1 MTris-HCl1reservoirpH8.5
430 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 22133 / Biso Wilson estimate: 28.6 Å2
Reflection
*PLUS
Highest resolution: 1.7 Å / % possible obs: 100 % / Redundancy: 4.1 % / Num. measured all: 300112 / Rmerge(I) obs: 0.059

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→5.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 950772.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2162 10 %RANDOM
Rwork0.231 ---
obs0.231 21621 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.0238 Å2 / ksol: 0.386122 e/Å3
Displacement parametersBiso mean: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å20.83 Å2
2---4.21 Å20 Å2
3---1.85 Å2
Refine analyzeLuzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→5.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 58 245 2113
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.8 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 347 9.7 %
Rwork0.308 3240 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2F_CHAIRB.PARAM
X-RAY DIFFRACTION3WATER.PARAM
X-RAY DIFFRACTION4ION.PARAM
Refinement
*PLUS
Highest resolution: 1.7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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