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- PDB-8ck2: MUC2 CysD1 G1352S -

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Basic information

Entry
Database: PDB / ID: 8ck2
TitleMUC2 CysD1 G1352S
ComponentsMucin-2
KeywordsSTRUCTURAL PROTEIN / mucin / disulfide bonds / calcium
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
WxxW domain / Mucin-2 protein WxxW repeating region / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / C-terminal cystine knot signature. ...WxxW domain / Mucin-2 protein WxxW repeating region / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / C-terminal cystine knot signature. / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain
Similarity search - Domain/homology
ACETATE ION / Mucin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKhmelnitsky, L. / Fass, D.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation2660/20 Israel
CitationJournal: To Be Published
Title: Pulmonary Fibrosis Mutation Undermines Mucin 5B Supramolecular Assembly
Authors: Khmelnitsky, L. / Javitt, G. / Reznik, N. / Yeshaya, N. / Elad, N. / Anikster, Y. / Shalva, N. / Barel, O. / Pode-Shakked, B. / Greenberg, L.J. / Segel, M.J. / Fass, D.
History
DepositionFeb 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mucin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0145
Polymers10,8521
Non-polymers1624
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-25 kcal/mol
Surface area6140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.008, 58.962, 27.659
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Mucin-2 / MUC-2 / Intestinal mucin-2


Mass: 10852.060 Da / Num. of mol.: 1 / Mutation: G1352S
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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM sodium acetate buffer, pH 4.6, 12% ethanol, 1% PEG 200, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.5→27.66 Å / Num. obs: 14727 / % possible obs: 97.92 % / Redundancy: 3.2 % / Biso Wilson estimate: 21.88 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06823 / Rpim(I) all: 0.04195 / Net I/σ(I): 8.95
Reflection shellResolution: 1.5→1.554 Å / Rmerge(I) obs: 0.7219 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 1443 / CC1/2: 0.723 / Rpim(I) all: 0.4398

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Processing

Software
NameVersionClassification
PHENIX1.20_4459phasing
PHENIX1.20_4459refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→27.66 Å / SU ML: 0.2529 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.7645
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2151 1308 8.89 %
Rwork0.1863 13400 -
obs0.1888 14727 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.52 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms733 0 7 93 833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073827
X-RAY DIFFRACTIONf_angle_d0.9821135
X-RAY DIFFRACTIONf_chiral_restr0.0629117
X-RAY DIFFRACTIONf_plane_restr0.0091156
X-RAY DIFFRACTIONf_dihedral_angle_d5.9883122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.560.48091480.4371446X-RAY DIFFRACTION97.91
1.56-1.630.36921390.31681485X-RAY DIFFRACTION98.9
1.63-1.720.32471390.23791480X-RAY DIFFRACTION98.78
1.72-1.820.25091430.21741443X-RAY DIFFRACTION97.48
1.82-1.970.22691520.20061499X-RAY DIFFRACTION99.34
1.97-2.160.20651390.16071499X-RAY DIFFRACTION98.73
2.16-2.480.24841430.17351481X-RAY DIFFRACTION97.77
2.48-3.120.18911550.17791521X-RAY DIFFRACTION98.13
3.12-27.660.17341500.16451546X-RAY DIFFRACTION94.75

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