+Open data
-Basic information
Entry | Database: PDB / ID: 6rbf | ||||||
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Title | Mucin 2 D3 domain | ||||||
Components | Mucin-2 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / Mucin 2 / extracellular / glycoprotein / D3 domain / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information inner mucus layer / outer mucus layer / host-mediated regulation of intestinal microbiota composition / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / maintenance of gastrointestinal epithelium / mucus secretion ...inner mucus layer / outer mucus layer / host-mediated regulation of intestinal microbiota composition / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / maintenance of gastrointestinal epithelium / mucus secretion / detoxification of copper ion / cupric ion binding / Dectin-2 family / cuprous ion binding / extracellular matrix / Golgi lumen / collagen-containing extracellular matrix / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å | ||||||
Authors | Javitt, G. / Fass, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2019 Title: Intestinal Gel-Forming Mucins Polymerize by Disulfide-Mediated Dimerization of D3 Domains. Authors: Javitt, G. / Calvo, M.L.G. / Albert, L. / Reznik, N. / Ilani, T. / Diskin, R. / Fass, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rbf.cif.gz | 617.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rbf.ent.gz | 414.8 KB | Display | PDB format |
PDBx/mmJSON format | 6rbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/6rbf ftp://data.pdbj.org/pub/pdb/validation_reports/rb/6rbf | HTTPS FTP |
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-Related structure data
Related structure data | 6n29S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 7 molecules ABCD
#1: Protein | Mass: 45899.297 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MUC2, SMUC / Production host: Homo sapiens (human) / References: UniProt: Q02817 #3: Sugar | |
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-Non-polymers , 4 types, 170 molecules
#2: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-SO4 / #6: 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: 3.05 Å3/Da / Density % sol: 59.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 105 mM lithium sulfate, 100 mM citrate/phosphate buffer, pH 4.2, 10% glycerol, and 14% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.704→48.35 Å / Num. obs: 62040 / % possible obs: 99.85 % / Redundancy: 13.5 % / Biso Wilson estimate: 49.49 Å2 / Rpim(I) all: 0.08746 / Net I/σ(I): 9.92 |
Reflection shell | Resolution: 2.704→2.801 Å / Redundancy: 13.4 % / Num. unique obs: 6087 / Rpim(I) all: 0.6062 / % possible all: 98.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6N29 Resolution: 2.704→48.35 Å / SU ML: 0.4513 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.704→48.35 Å
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Refine LS restraints |
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LS refinement shell |
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