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Yorodumi- PDB-3n3f: Crystal Structure of the Human Collagen XV Trimerization Domain: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n3f | ||||||
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Title | Crystal Structure of the Human Collagen XV Trimerization Domain: A Potent Trimerizing Unit Common to Multiplexin Collagens | ||||||
Components | Collagen alpha-1(XV) chain | ||||||
Keywords | PROTEIN BINDING / collagen / extracellular matrix / basement membrane / collagen XV / trimerization domain / folding / association / chain selection / triple helix / multiplexin / collagen XVIII | ||||||
Function / homology | Function and homology information collagen type XV trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / endothelial cell morphogenesis / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / collagen catabolic process / extracellular matrix ...collagen type XV trimer / Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / endothelial cell morphogenesis / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / collagen catabolic process / extracellular matrix / extracellular matrix organization / angiogenesis / collagen-containing extracellular matrix / membrane => GO:0016020 / cell adhesion / endoplasmic reticulum lumen / signal transduction / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.005 Å | ||||||
Authors | Wirz, J.A. | ||||||
Citation | Journal: Matrix Biol. / Year: 2011 Title: Crystal structure of the human collagen XV trimerization domain: A potent trimerizing unit common to multiplexin collagens. Authors: Wirz, J.A. / Boudko, S.P. / Lerch, T.F. / Chapman, M.S. / Bachinger, H.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n3f.cif.gz | 34.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n3f.ent.gz | 23.3 KB | Display | PDB format |
PDBx/mmJSON format | 3n3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/3n3f ftp://data.pdbj.org/pub/pdb/validation_reports/n3/3n3f | HTTPS FTP |
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-Related structure data
Related structure data | 3hshS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6259.278 Da / Num. of mol.: 2 / Fragment: UNP residues 1133-1186 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: COL15A1 / Plasmid: pET23-HisTag-Trx / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39059 #2: 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: 1.82 Å3/Da / Density % sol: 32.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris, 0.2 M MgCl2, 30% (w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 19, 2009 |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.005→42.539 Å / Num. all: 6095 / Num. obs: 6095 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 22.838 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 35.4 |
Reflection shell | Resolution: 2.005→2.01 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 15.6 / Num. unique all: 881 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.49 / Cor.coef. Fo:Fc: 0.48
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 3HSH Resolution: 2.005→35.69 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ANISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 52.109 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 65.98 Å2 / Biso mean: 26.816 Å2 / Biso min: 8.63 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.005→35.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.005→2.07 Å
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Xplor file |
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