+Open data
-Basic information
Entry | Database: PDB / ID: 4ihk | ||||||
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Title | Crystal structure of the Collagen VI alpha3 N5 domain R1061Q | ||||||
Components | Collagen alpha3(VI) | ||||||
Keywords | CELL ADHESION / Collagen VI 3N5 / VWA | ||||||
Function / homology | Function and homology information NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / ECM proteoglycans / Integrin cell surface interactions / collagen trimer / response to glucose ...NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / ECM proteoglycans / Integrin cell surface interactions / collagen trimer / response to glucose / extracellular matrix / sarcolemma / serine-type endopeptidase inhibitor activity / collagen-containing extracellular matrix / cell adhesion / extracellular space Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Mikolajek, H. / Becker, A.K.A. / Paulsson, M. / Wagener, R. / Werner, J.M. | ||||||
Citation | Journal: Structure / Year: 2014 Title: A structure of a collagen VI VWA domain displays N and C termini at opposite sides of the protein Authors: Becker, A.K. / Mikolajek, H. / Paulsson, M. / Wagener, R. / Werner, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ihk.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ihk.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ihk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/4ihk ftp://data.pdbj.org/pub/pdb/validation_reports/ih/4ihk | HTTPS FTP |
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-Related structure data
Related structure data | 4igiSC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21682.645 Da / Num. of mol.: 1 / Fragment: Collagen VI Alpha3 N5m, UNP residues 1022-1224 / Mutation: G1061R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57Bl6 / Gene: Col6a3 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q9Z0I9, UniProt: E9PWQ3*PLUS |
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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: 1.87 Å3/Da / Density % sol: 34.17 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.2M sodium chloride, 0.1M phosphate/citrate, 20% PEG 8000, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2012 |
Radiation | Monochromator: ACCEL Fixed exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→38.35 Å / Num. all: 53401 / Num. obs: 53401 / % possible obs: 99.7 % / Observed criterion σ(I): 19.3 / Redundancy: 6.6 % / Biso Wilson estimate: 11.09 Å2 / Rmerge(I) obs: 0.04 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3739 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4IGI Resolution: 1.2→38.349 Å / SU ML: 0.09 / σ(F): 1.35 / Phase error: 14.2 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→38.349 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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