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Yorodumi- PDB-2w86: Crystal structure of fibrillin-1 domains cbEGF9hyb2cbEGF10, calci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w86 | ||||||
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Title | Crystal structure of fibrillin-1 domains cbEGF9hyb2cbEGF10, calcium saturated form | ||||||
Components | FIBRILLIN-1 | ||||||
Keywords | GLYCOPROTEIN / FIBRILLIN / PHOSPHOPROTEIN / EGF-LIKE DOMAIN / DISEASE MUTATION / CRANIOSYNOSTOSIS / EXTRACELLULAR MATRIX / FIBRILLIN CALCIUM CBEGF HYBRID / CALCIUM / SECRETED / POLYMORPHISM | ||||||
Function / homology | Function and homology information post-embryonic eye morphogenesis / extracellular matrix constituent conferring elasticity / sequestering of BMP in extracellular matrix / sequestering of TGFbeta in extracellular matrix / microfibril / embryonic eye morphogenesis / negative regulation of osteoclast development / metanephros development / Elastic fibre formation / camera-type eye development ...post-embryonic eye morphogenesis / extracellular matrix constituent conferring elasticity / sequestering of BMP in extracellular matrix / sequestering of TGFbeta in extracellular matrix / microfibril / embryonic eye morphogenesis / negative regulation of osteoclast development / metanephros development / Elastic fibre formation / camera-type eye development / Molecules associated with elastic fibres / cellular response to insulin-like growth factor stimulus / cell adhesion mediated by integrin / extracellular matrix structural constituent / negative regulation of osteoclast differentiation / TGF-beta receptor signaling activates SMADs / basement membrane / anatomical structure morphogenesis / Integrin cell surface interactions / cellular response to transforming growth factor beta stimulus / extracellular matrix / Degradation of the extracellular matrix / skeletal system development / Post-translational protein phosphorylation / hormone activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / integrin binding / heparin binding / heart development / collagen-containing extracellular matrix / endoplasmic reticulum lumen / calcium ion binding / protein-containing complex binding / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Jensen, S.A. / Iqbal, S. / Lowe, E.D. / Redfield, C. / Handford, P.A. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Structure and Interdomain Interactions of a Hybrid Domain: A Disulphide-Rich Module of the Fibrillin/Ltbp Superfamily of Matrix Proteins. Authors: Jensen, S.A. / Iqbal, S. / Lowe, E.D. / Redfield, C. / Handford, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w86.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w86.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 2w86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/2w86 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/2w86 | HTTPS FTP |
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-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 | Mass: 15527.713 Da / Num. of mol.: 1 / Fragment: CBEGF9HYB2CBEGF10, RESIDUES 807-951 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P35555 | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE DEPOSITED STRUCTURE CONTAINS ONLY THE CBEGF9HYB2CBEGF10 DOMAINS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.2 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 100 MM TRIS PH 7.5, 200 MM NAI, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.04 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 13, 2008 |
Radiation | Monochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.79 Å / Num. obs: 15382 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Biso Wilson estimate: 14.46 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 7.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.8→41.75 Å / SU ML: 0.23 / σ(F): 0.09 / Phase error: 19.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.373 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.19 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→41.75 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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