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- PDB-6xfi: Crystal Structures of beta-1,4-N-Acetylglucosaminyltransferase 2 ... -

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Basic information

Entry
Database: PDB / ID: 6xfi
TitleCrystal Structures of beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2): Structural Basis for Inherited Muscular Dystrophies
ComponentsProtein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
KeywordsTRANSFERASE / muscular dystrophy / alpha-dystroglycan / O-mannosylation / POMGNT2
Function / homology
Function and homology information


protein O-mannose beta-1,4-N-acetylglucosaminyltransferase / O-linked glycosylation / protein O-linked glycosylation via mannose / protein O-acetylglucosaminyltransferase activity / acetylglucosaminyltransferase activity / protein O-linked glycosylation / neuron migration / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Glycosyltransferase 61 / : / Glycosyltransferase 61 / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE / Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHalmo, S.M. / Yeh, J. / Wells, L. / Moremen, K.W. / Lanzilotta, W.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111939-05 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Crystal structures of beta-1,4-N-acetylglucosaminyltransferase 2: structural basis for inherited muscular dystrophies.
Authors: Yang, J.Y. / Halmo, S.M. / Praissman, J. / Chapla, D. / Singh, D. / Wells, L. / Moremen, K.W. / Lanzilotta, W.N.
History
DepositionJun 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8785
Polymers61,0621
Non-polymers8154
Water3,495194
1
A: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
hetero molecules

A: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,75610
Polymers122,1252
Non-polymers1,6318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area8560 Å2
ΔGint-55 kcal/mol
Surface area43000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.840, 129.840, 81.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 / POMGnT2 / Extracellular O-linked N-acetylglucosamine transferase-like / Glycosyltransferase-like ...POMGnT2 / Extracellular O-linked N-acetylglucosamine transferase-like / Glycosyltransferase-like domain-containing protein 2


Mass: 61062.449 Da / Num. of mol.: 1 / Fragment: UNP residues 52-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2 / Cell line (production host): HEK293S / Production host: Homo sapiens (human)
References: UniProt: Q8NAT1, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.1 M potassium/sodium tartrate, 0.1 M Bis-Tris, pH 7.5, 10% PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 49420 / % possible obs: 99.7 % / Redundancy: 11.3 % / CC1/2: 1 / CC star: 1 / Net I/σ(I): 27.5
Reflection shellResolution: 1.97→2.08 Å / Num. unique obs: 4759 / CC1/2: 0.298 / CC star: 0.678

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→40 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 1930 4.07 %
Rwork0.1979 45539 -
obs0.1991 47469 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.17 Å2 / Biso mean: 40.1046 Å2 / Biso min: 16.41 Å2
Refinement stepCycle: final / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 49 194 4385
Biso mean--55.95 42.38 -
Num. residues----511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.37241340.29223158329298
2.05-2.110.34771340.26223161329599
2.11-2.170.25971360.244631993335100
2.17-2.240.28271360.23232093345100
2.24-2.320.29191360.239732333369100
2.32-2.410.25791370.235732083345100
2.41-2.520.29781360.223832263362100
2.52-2.650.25141380.222132303368100
2.65-2.820.26051370.220132543391100
2.82-3.040.22031380.206432513389100
3.04-3.340.22091380.20332803418100
3.34-3.820.21051400.175232933433100
3.82-4.820.18371410.155133343475100
4.82-400.19151490.181535033652100

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