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- PDB-6rbf: Mucin 2 D3 domain -

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Basic information

Entry
Database: PDB / ID: 6rbf
TitleMucin 2 D3 domain
ComponentsMucin-2
KeywordsANTIMICROBIAL 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
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å
AuthorsJavitt, G. / Fass, D.
CitationJournal: 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
DepositionApr 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 29, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mucin-2
B: Mucin-2
C: Mucin-2
D: Mucin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,27420
Polymers183,5974
Non-polymers1,67716
Water2,828157
1
A: Mucin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2534
Polymers45,8991
Non-polymers3533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mucin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8549
Polymers45,8991
Non-polymers9558
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mucin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0353
Polymers45,8991
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mucin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1324
Polymers45,8991
Non-polymers2323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.461, 156.925, 93.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

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Protein / Sugars , 2 types, 7 molecules ABCD

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


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 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.: 3
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 4 types, 170 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.704→2.801 Å / Redundancy: 13.4 % / Num. unique obs: 6087 / Rpim(I) all: 0.6062 / % possible all: 98.93

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N29

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
RfactorNum. reflection% reflection
Rfree0.2833 5915 5 %
Rwork0.2166 --
obs0.2199 62027 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.43 Å2
Refinement stepCycle: LAST / Resolution: 2.704→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10737 0 94 157 10988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014311199
X-RAY DIFFRACTIONf_angle_d1.322715315
X-RAY DIFFRACTIONf_chiral_restr0.06451665
X-RAY DIFFRACTIONf_plane_restr0.00911971
X-RAY DIFFRACTIONf_dihedral_angle_d15.2426719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.45161830.38853604X-RAY DIFFRACTION95.49
2.73-2.770.41131850.34123774X-RAY DIFFRACTION100
2.77-2.80.35352050.32233780X-RAY DIFFRACTION99.97
2.8-2.840.3671820.31143724X-RAY DIFFRACTION99.95
2.84-2.870.41941760.31383811X-RAY DIFFRACTION99.97
2.87-2.910.30422220.29373727X-RAY DIFFRACTION99.95
2.91-2.950.32081620.27223747X-RAY DIFFRACTION99.97
2.95-30.27561830.25993770X-RAY DIFFRACTION100
3-3.040.32252270.26073723X-RAY DIFFRACTION99.92
3.04-3.090.32792450.25983761X-RAY DIFFRACTION99.98
3.09-3.150.33572520.25873669X-RAY DIFFRACTION99.97
3.15-3.210.34042190.25023735X-RAY DIFFRACTION100
3.21-3.270.28531760.24683791X-RAY DIFFRACTION99.97
3.27-3.330.32551740.24573760X-RAY DIFFRACTION99.97
3.33-3.410.32332220.24413713X-RAY DIFFRACTION100
3.41-3.490.31641890.22693773X-RAY DIFFRACTION99.92
3.49-3.570.26251660.21413784X-RAY DIFFRACTION99.97
3.57-3.670.35441720.22323782X-RAY DIFFRACTION99.75
3.67-3.780.27432240.20913694X-RAY DIFFRACTION99.44
3.78-3.90.25862220.19193775X-RAY DIFFRACTION100
3.9-4.040.242030.18123736X-RAY DIFFRACTION100
4.04-4.20.23651610.17223769X-RAY DIFFRACTION100
4.2-4.390.23451760.16343779X-RAY DIFFRACTION100
4.39-4.620.21691990.14773757X-RAY DIFFRACTION100
4.62-4.910.18682190.14373735X-RAY DIFFRACTION99.97
4.91-5.290.22091780.15533780X-RAY DIFFRACTION100
5.29-5.820.23111590.17713813X-RAY DIFFRACTION100
5.82-6.660.26212030.19893744X-RAY DIFFRACTION100
6.66-8.390.26942160.21383726X-RAY DIFFRACTION100
8.39-49.490.3362150.25763736X-RAY DIFFRACTION99.7

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