+Open data
-Basic information
Entry | Database: PDB / ID: 1vdf | ||||||
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Title | ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN | ||||||
Components | CARTILAGE OLIGOMERIC MATRIX PROTEIN | ||||||
Keywords | EXTRACELLULAR MATRIX PROTEIN / ASSEMBLY DOMAIN / CARTILAGE / OLIGOMERIC MATRIX PROTEIN / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information cartilage homeostasis / Integrin cell surface interactions / tendon development / negative regulation of hemostasis / ECM proteoglycans / musculoskeletal movement / vascular associated smooth muscle contraction / vascular associated smooth muscle cell development / chondrocyte development / bone growth ...cartilage homeostasis / Integrin cell surface interactions / tendon development / negative regulation of hemostasis / ECM proteoglycans / musculoskeletal movement / vascular associated smooth muscle contraction / vascular associated smooth muscle cell development / chondrocyte development / bone growth / BMP binding / chondrocyte proliferation / endochondral bone growth / growth plate cartilage development / 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 / artery morphogenesis / neuromuscular process / 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 / 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 | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.05 Å | ||||||
Authors | Malashkevich, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vdf.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vdf.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 1vdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/1vdf ftp://data.pdbj.org/pub/pdb/validation_reports/vd/1vdf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | 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 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 36 % / Description: MOLECULAR REPLACEMENT WAS NOT USED. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: 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 dropDetails: Efimov, V.P., (1996) Proteins: Struct.,Funct., Genet., 24, 259. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 279 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 1994 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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.
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Solvent computation | Solvent model: TNT / Bsol: 171.3 Å2 / ksol: 0.826 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.176 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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