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- PDB-7prl: MUC2 D1 with Cu(II) -

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Basic information

Entry
Database: PDB / ID: 7prl
TitleMUC2 D1 with Cu(II)
ComponentsMucin-2
KeywordsANTIMICROBIAL PROTEIN / Mucin 2 / Mucin-2 / MUC2 / copper / Cu / Cu(II)
Function / homology
Function and homology information


extracellular matrix / extracellular space
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
COPPER (II) ION / Mucin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsReznik, N. / Fass, D.
Funding support1items
OrganizationGrant numberCountry
Israel Science Foundation2660/20
CitationJournal: Cell / Year: 2022
Title: Intestinal mucin is a chaperone of multivalent copper.
Authors: Reznik, N. / Gallo, A.D. / Rush, K.W. / Javitt, G. / Fridmann-Sirkis, Y. / Ilani, T. / Nairner, N.A. / Fishilevich, S. / Gokhman, D. / Chacon, K.N. / Franz, K.J. / Fass, D.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)44,1297
Polymers43,4761
Non-polymers6536
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint1 kcal/mol
Surface area17990 Å2
Unit cell
Length a, b, c (Å)95.900, 141.210, 68.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Mucin-2 /


Mass: 43475.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC2 / Production host: Homo sapiens (human) / References: UniProt: A0A0G2JR65
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 30 mM MgCl2, 8% polyethylene glycol 3350, 100 mM citrate buffer, pH 5.4, and 10% glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.48→49.17 Å / Num. obs: 16761 / % possible obs: 99.16 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 9.69
Reflection shellResolution: 2.48→2.569 Å / Num. unique obs: 1650 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6tm2

6tm2


Resolution: 2.48→49.172 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2604 850 5.08 %
Rwork0.1862 15892 -
obs0.19 16742 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.68 Å2 / Biso mean: 53.6254 Å2 / Biso min: 21.17 Å2
Refinement stepCycle: final / Resolution: 2.48→49.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 39 79 2831
Biso mean--77.61 49.53 -
Num. residues----357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4801-2.63550.33381540.2332259299
2.6355-2.8390.35841380.24572623100
2.839-3.12460.29361330.2261263799
3.1246-3.57670.28681220.1987265699
3.5767-4.50580.23281500.1616265299
4.5058-49.1720.22061530.1601273298

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