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- PDB-6xi2: Apo form of POMGNT2 -

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Basic information

Entry
Database: PDB / ID: 6xi2
TitleApo form of POMGNT2
Components
  • (Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase ...) x 4
  • ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
  • ALA-GLY-ALA-GLY-ALA-ALA-ALA-ALA-ALA-ALA
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 / Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.57 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) 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 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
B: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
D: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
C: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
G: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
H: ALA-GLY-ALA-GLY-ALA-ALA-ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,84134
Polymers243,8036
Non-polymers3,03828
Water2,666148
1
A: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
B: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
H: ALA-GLY-ALA-GLY-ALA-ALA-ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,73119
Polymers121,9593
Non-polymers1,77216
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
C: Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2
G: ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,11015
Polymers121,8443
Non-polymers1,26612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.322, 153.979, 187.494
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase ... , 4 types, 4 molecules ABDC

#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: 61017.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2 / Production host: Homo sapiens (human)
References: UniProt: Q8NAT1, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase
#2: 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: 60240.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2 / Production host: Homo sapiens (human)
References: UniProt: Q8NAT1, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase
#3: 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: 60972.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2 / Production host: Homo sapiens (human)
References: UniProt: Q8NAT1, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase
#4: 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: 60143.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2 / Production host: Homo sapiens (human)
References: UniProt: Q8NAT1, protein O-mannose beta-1,4-N-acetylglucosaminyltransferase

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Protein/peptide , 2 types, 2 molecules GH

#5: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 728.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Protein/peptide ALA-GLY-ALA-GLY-ALA-ALA-ALA-ALA-ALA-ALA


Mass: 700.741 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 1 types, 3 molecules

#7: 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.: 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 , 2 types, 173 molecules

#8: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.29 Å3/Da / Density % sol: 71.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M potassium/sodium tartrate, 0.1 M Bis-Tris, pH 7.9, 10% PEG8000

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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: RAYONIX MX300HE / Detector: CCD / Date: Feb 13, 2016
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: 2.57→50 Å / Num. obs: 131723 / % possible obs: 99.1 % / Redundancy: 14.6 % / CC1/2: 0.864 / CC star: 0.963 / Net I/σ(I): 21.3
Reflection shellResolution: 2.57→2.66 Å / Num. unique obs: 12111 / CC1/2: 0.864 / CC star: 0.963

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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: 2.57→45.99 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 2018 1.55 %
Rwork0.2135 128275 -
obs0.2138 130293 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.08 Å2 / Biso mean: 48.964 Å2 / Biso min: 21.21 Å2
Refinement stepCycle: final / Resolution: 2.57→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16873 0 167 148 17188
Biso mean--67.95 42.2 -
Num. residues----2106
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 (%)
2.57-2.630.31731500.258203835390
2.63-2.70.27841300.24389147927799
2.7-2.780.27481350.251790989233100
2.78-2.870.29921540.255891579311100
2.87-2.970.32031430.259791279270100
2.97-3.090.33591400.25191889328100
3.09-3.230.25371530.246691909343100
3.23-3.40.24441440.238591859329100
3.4-3.620.24221380.209892269364100
3.62-3.90.21471520.194892389390100
3.9-4.290.19971410.18692649405100
4.29-4.910.19341450.17593329477100
4.91-6.180.21191460.198993909536100
6.18-45.990.22521470.21279530967798

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