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- PDB-1vdf: ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1vdf
TitleASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN
ComponentsCARTILAGE OLIGOMERIC MATRIX PROTEIN
KeywordsEXTRACELLULAR MATRIX PROTEIN / ASSEMBLY DOMAIN / CARTILAGE / OLIGOMERIC MATRIX PROTEIN / GLYCOPROTEIN
Function / homology
Function and homology information


tendon development / negative regulation of hemostasis / cartilage homeostasis / Integrin cell surface interactions / ECM proteoglycans / vascular associated smooth muscle contraction / chondrocyte development / bone growth / vascular associated smooth muscle cell development / musculoskeletal movement ...tendon development / negative regulation of hemostasis / cartilage homeostasis / Integrin cell surface interactions / ECM proteoglycans / vascular associated smooth muscle contraction / chondrocyte development / bone growth / vascular associated smooth muscle cell development / musculoskeletal movement / BMP binding / chondrocyte proliferation / growth plate cartilage development / endochondral bone growth / positive regulation of chondrocyte proliferation / vitamin D binding / regulation of bone mineralization / muscle cell development / heparan sulfate proteoglycan binding / bone morphogenesis / cartilage development / collagen fibril organization / proteoglycan binding / limb development / artery morphogenesis / extracellular matrix structural constituent / neuromuscular process / skin development / bone mineralization / fibronectin binding / protein secretion / response to unfolded protein / BMP signaling pathway / collagen binding / extracellular matrix / ossification / skeletal system development / protein homooligomerization / protein processing / platelet aggregation / multicellular organism growth / integrin binding / blood coagulation / cellular senescence / heparin binding / : / regulation of gene expression / 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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cartilage oligomeric matrix protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.05 Å
AuthorsMalashkevich, V.N.
Citation
Journal: Science / Year: 1996
Title: The crystal structure of a five-stranded coiled coil in COMP: a prototype ion channel?
Authors: Malashkevich, V.N. / Kammerer, R.A. / Efimov, V.P. / Schulthess, T. / Engel, J.
#1: Journal: Proteins / Year: 1996
Title: Crystallization and Preliminary Crystallographic Study of the Pentamerizing Domain from Cartilage Oligomeric Matrix Protein: A Five-Stranded Alpha-Helical Bundle
Authors: Efimov, V.P. / Engel, J. / Malashkevich, V.N.
History
DepositionSep 12, 1996Processing site: BNL
Revision 1.0Oct 8, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_ref_seq_dif.details / _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: 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)26,5316
Polymers26,4965
Non-polymers351
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-130 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.470, 49.470, 54.980
Angle α, β, γ (deg.)90.00, 103.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
CARTILAGE OLIGOMERIC MATRIX PROTEIN / COMP


Mass: 5299.129 Da / Num. of mol.: 5 / Fragment: ASSEMBLY DOMAIN
Source method: isolated from a genetically manipulated source
Details: PENTAMERIC COILED-COIL / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: CARTILAGE / Cell line: BL21 / Plasmid: PET-3B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P35444
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 36 % / Description: MOLECULAR REPLACEMENT WAS NOT USED.
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 17% PEG-1500, 50 MM NA-PI, PH 6.0, 0.5M NACL, HANGING DROP, vapor diffusion - hanging drop
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Details: Efimov, V.P., (1996) Proteins: Struct.,Funct., Genet., 24, 259.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116-17 %PEG15001reservoir
20.5 M1reservoirNaCl
350 mMsodium phosphate1reservoir
413 mg/mlprotein1drop
510 mMTris-HCl1drop
6200 mM1dropNaCl
716-17 %PEG15001drop
80.5 M1dropNaCl
950 mMsodium phosphate1drop

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 12978 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 10.5
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.21 / % possible all: 81
Reflection
*PLUS
Num. measured all: 46638

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
TNTrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.05→8 Å / Isotropic thermal model: TNT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: MET 27 AND GLY 72 ARE DISORDERED IN ALL FIVE CHAINS OF THE CRYSTAL STRUCTURE. ALTHOUGH THEY WERE MODELED BASED ON THE EXISTING MAP, THEIR CONFORMATIONS ARE NOT SECURE. GLU 28 IN CHAIN D HAS ...Details: MET 27 AND GLY 72 ARE DISORDERED IN ALL FIVE CHAINS OF THE CRYSTAL STRUCTURE. ALTHOUGH THEY WERE MODELED BASED ON THE EXISTING MAP, THEIR CONFORMATIONS ARE NOT SECURE. GLU 28 IN CHAIN D HAS UNFAVORABLE PHI-PSI TORSION ANGLES. IT IS POORLY DEFINED IN THE ELECTRON DENSITY MAP.
RfactorNum. reflection% reflection
Rwork0.176 --
all-12978 -
obs-12978 95.1 %
Solvent computationSolvent model: TNT / Bsol: 171.3 Å2 / ksol: 0.826 e/Å3
Refinement stepCycle: LAST / Resolution: 2.05→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 1 169 2000
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01236800.02
X-RAY DIFFRACTIONt_angle_deg1.4349301.9
X-RAY DIFFRACTIONt_dihedral_angle_d17.99234015
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0061600.02
X-RAY DIFFRACTIONt_gen_planes0.0084900.02
X-RAY DIFFRACTIONt_it6.06186.67
X-RAY DIFFRACTIONt_nbd0.035440.1
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0060.02
X-RAY DIFFRACTIONt_plane_restr0.0080.02

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