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Yorodumi- PDB-7xan: Structure of a triple-helix region of human collagen type III fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xan | ||||||
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Title | Structure of a triple-helix region of human collagen type III from Trautec | ||||||
Components | Collagen alpha-1(III) chain | ||||||
Keywords | STRUCTURAL PROTEIN / Human collagen type III / Triple-helix region / Integrin recognition motif | ||||||
Function / homology | Function and homology information collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding / endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength ...collagen type III trimer / aorta smooth muscle tissue morphogenesis / limb joint morphogenesis / transforming growth factor beta1 production / elastic fiber assembly / negative regulation of neuron migration / Collagen chain trimerization / platelet-derived growth factor binding / endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / basement membrane organization / Extracellular matrix organization / layer formation in cerebral cortex / Collagen biosynthesis and modifying enzymes / peptide cross-linking / tissue homeostasis / Signaling by PDGF / negative regulation of immune response / NCAM1 interactions / digestive tract development / response to angiotensin / collagen fibril organization / Scavenging by Class A Receptors / extracellular matrix structural constituent / skin development / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / Syndecan interactions / positive regulation of Rho protein signal transduction / SMAD binding / Collagen degradation / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / chondrocyte differentiation / supramolecular fiber organization / extracellular matrix organization / cell-matrix adhesion / transforming growth factor beta receptor signaling pathway / response to cytokine / integrin-mediated signaling pathway / cellular response to amino acid stimulus / neuron migration / lung development / wound healing / response to radiation / multicellular organism growth / cerebral cortex development / platelet activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / heart development / fibroblast proliferation / collagen-containing extracellular matrix / in utero embryonic development / protease binding / endoplasmic reticulum lumen / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Qian, S. / Li, H. / Fan, X. / Tian, X. / Li, J. / Wang, L. / Chu, Y. | ||||||
Citation | Journal: To Be Published Title: Structure of a triple-helix region of human collagen type III from Trautec Authors: Qian, S. / Li, H. / Fan, X. / Tian, X. / Li, J. / Wang, L. / Chu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xan.cif.gz | 26.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xan.ent.gz | 17.7 KB | Display | PDB format |
PDBx/mmJSON format | 7xan.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/7xan ftp://data.pdbj.org/pub/pdb/validation_reports/xa/7xan | HTTPS FTP |
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-Related structure data
Related structure data | 7wwrC 7wwsC 2cuoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2434.551 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02461 #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.74 Å3/Da / Density % sol: 29.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.04M K phosphate monobasic, 16% w/v PEG 8000, 20% v/v Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.7749 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 18, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→41.49 Å / Num. obs: 8076 / % possible obs: 97.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 48.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.058 / Num. unique obs: 360 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2cuo Resolution: 1.5→20.755 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.114 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.084 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.368 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→20.755 Å
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Refine LS restraints |
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LS refinement shell |
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