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Yorodumi- PDB-1uzq: Integrin binding cbEGF22-TB4-cbEGF33 fragment of human fibrillin-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uzq | ||||||
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Title | Integrin binding cbEGF22-TB4-cbEGF33 fragment of human fibrillin-1, apo form cbEGF23 domain only. | ||||||
Components | FIBRILLIN-1 | ||||||
Keywords | MATRIX PROTEIN / EXTRA-CELLULAR MATRIX / FIBRILLIN-1 / CBEGF DOMAIN / TB DOMAIN MATRIX PROTEIN | ||||||
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 / Degradation of the extracellular matrix / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Lee, S.S.J. / Knott, V. / Harlos, K. / Handford, P.A. / Stuart, D.I. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Structure of the Integrin Binding Fragment from Fibrillin-1 Gives New Insights Into Microfibril Organization Authors: Lee, S.S.J. / Knott, V. / Jovanovi, J. / Harlos, K. / Grimes, J. / Choulier, L. / Mardon, H. / Stuart, D.I. / 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 | 1uzq.cif.gz | 40.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uzq.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 1uzq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/1uzq ftp://data.pdbj.org/pub/pdb/validation_reports/uz/1uzq | HTTPS FTP |
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-Related 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: 17332.436 Da / Num. of mol.: 1 / Fragment: BEGF22-TB4-CBEGF23, RESIDUES 1486-1647 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: EXTRA-ELLULAR MATRIX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P35555 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 41 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: SITTING DROP VAPOUR DIFFUSION, 3 MICROLITRE OF 25MG/ML PROTEIN, 10MM TRIS PH7.5 + 0.5 MICROLITRES OF 40% V/V POLYPROPYLENE GLYCOL P400 + 2.5 MICROLITRES RESERVOIR SOLUTION (0.2M LISULFATE, 0. ...Details: SITTING DROP VAPOUR DIFFUSION, 3 MICROLITRE OF 25MG/ML PROTEIN, 10MM TRIS PH7.5 + 0.5 MICROLITRES OF 40% V/V POLYPROPYLENE GLYCOL P400 + 2.5 MICROLITRES RESERVOIR SOLUTION (0.2M LISULFATE, 0.1M TRIS PH 8.5, 30% PEG 4000) BOTH PROTEIN AND RESERVOIR SOLUTIONS CONTAINED 5MM EDTA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542 |
Detector | Type: MARRESEARCH 300MM / Detector: IMAGE PLATE / Date: Dec 15, 2001 / Details: OSMIC BLUE CONFOCAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 6275 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 5.8 / % possible all: 98.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PBD FIBRILLIN SM BOUND FORM Resolution: 2.4→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 80 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 Å / Total num. of bins used: 13 /
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