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Yorodumi- PDB-1fbm: ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN IN COMPLEX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fbm | ||||||
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Title | ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN IN COMPLEX WITH ALL-TRANS RETINOL | ||||||
Components | PROTEIN (CARTILAGE OLIGOMERIC MATRIX PROTEIN) | ||||||
Keywords | CELL ADHESION / EXTRACELLULAR MATRIX PROTEIN / ASSEMBLY DOMAIN / CARTILAGE / OLIGOMERIC MATRIX PROTEIN / GLYCOPROTEIN / RETINOL-COMPLEX | ||||||
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 / BMP signaling pathway / bone mineralization / fibronectin binding / response to unfolded protein / protein secretion / ossification / collagen binding / skeletal system development / protein homooligomerization / multicellular organism growth / cellular senescence / protein processing / platelet aggregation / integrin binding / blood coagulation / regulation of gene expression / heparin binding / 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 / Resolution: 2.7 Å | ||||||
Authors | Guo, Y. / Bozic, D. / Malashkevich, V.N. / Kammerer, R.A. / Schulthess, T. | ||||||
Citation | Journal: EMBO J. / Year: 1998 Title: All-trans retinol, vitamin D and other hydrophobic compounds bind in the axial pore of the five-stranded coiled-coil domain of cartilage oligomeric matrix protein. Authors: Guo, Y. / Bozic, D. / Malashkevich, V.N. / Kammerer, R.A. / Schulthess, T. #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. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fbm.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fbm.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 1fbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fbm_validation.pdf.gz | 450.6 KB | Display | wwPDB validaton report |
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Full document | 1fbm_full_validation.pdf.gz | 460.1 KB | Display | |
Data in XML | 1fbm_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 1fbm_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/1fbm ftp://data.pdbj.org/pub/pdb/validation_reports/fb/1fbm | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-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 / 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-RTL / | #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: 1.92 Å3/Da / Density % sol: 35.83 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: COMPcc (16 mg/ml) in 20 mM sodium phosphate, 200 mM NaCl (pH 7.5) precipitant: 7-8% PEG 8000, 50 mM sodium cacodylate (pH 6.0), 50 mM sodium acetate, 50 mM calcium acetate , VAPOR DIFFUSION, ...Details: COMPcc (16 mg/ml) in 20 mM sodium phosphate, 200 mM NaCl (pH 7.5) precipitant: 7-8% PEG 8000, 50 mM sodium cacodylate (pH 6.0), 50 mM sodium acetate, 50 mM calcium acetate , VAPOR DIFFUSION, HANGING DROP, temperature 20.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→3 Å / Num. all: 5464 / Num. obs: 5464 / % possible obs: 86 % / Redundancy: 3.71 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.132 |
Reflection shell | Resolution: 2.7→3 Å / Num. unique all: 5464 / % possible all: 87.6 |
Reflection | *PLUS Num. measured all: 20313 |
Reflection shell | *PLUS % possible obs: 87.6 % |
-Processing
Software |
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Refinement | Resolution: 2.7→3 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→3 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||
Refine LS restraints | *PLUS
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