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- PDB-5ggl: Crystal structure of N-terminal domain of human protein O-mannose... -

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Basic information

Entry
Database: PDB / ID: 5ggl
TitleCrystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-alpha-pNP
ComponentsProtein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
KeywordsSUGAR BINDING PROTEIN / glycosyltransferease / O-mannosylation / alpha-dystroglycan
Function / homology
Function and homology information


beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / O-linked glycosylation / localization of cell / protein O-linked glycosylation via N-acetyl-galactosamine / protein O-linked glycosylation via mannose / reactive gliosis / acetylglucosaminyltransferase activity / basement membrane organization / dentate gyrus development ...beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / O-linked glycosylation / localization of cell / protein O-linked glycosylation via N-acetyl-galactosamine / protein O-linked glycosylation via mannose / reactive gliosis / acetylglucosaminyltransferase activity / basement membrane organization / dentate gyrus development / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / myelination / sensory perception of sound / manganese ion binding / carbohydrate binding / gene expression / Golgi membrane / membrane
Similarity search - Function
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1, PANDER-like domain / : / Glycosyl transferase, family 13 / ILEI/PANDER domain / GNT-I family / Interleukin-like EMT inducer / GG-type lectin domain profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Chem-6ZC / Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsKuwabara, N. / Senda, T. / Kato, R.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS26840029 Japan
JSPS16K07284 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan
Authors: Kuwabara, N. / Manya, H. / Yamada, T. / Tateno, H. / Kanagawa, M. / Kobayashi, K. / Akasaka-Manya, K. / Hirose, Y. / Mizuno, M. / Ikeguchi, M. / Toda, T. / Hirabayashi, J. / Senda, T. / Endo, T. / Kato, R.
History
DepositionJun 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,9314
Polymers35,2462
Non-polymers6852
Water5,639313
1
A: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9652
Polymers17,6231
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9652
Polymers17,6231
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.330, 68.686, 88.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

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Components

#1: Protein Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 / POMGnT1 / UDP-GlcNAc:alpha-D-mannoside beta-1 / 2-N-acetylglucosaminyltransferase I.2 / GnT I.2


Mass: 17623.020 Da / Num. of mol.: 2 / Fragment: UNP residues 92-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT1, MGAT1.2, UNQ746/PRO1475 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8WZA1, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Sugar ChemComp-6ZC / 4-nitrophenyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside / N-[(2R,3R,4R,5S,6R)-6-(hydroxymethyl)-2-(4-nitrophenoxy)-4,5-bis(oxidanyl)oxan-3-yl]ethanamide / 4-nitrophenyl 2-acetamido-2-deoxy-alpha-D-glucoside / 4-nitrophenyl 2-acetamido-2-deoxy-D-glucoside / 4-nitrophenyl 2-acetamido-2-deoxy-glucoside


Type: D-saccharide / Mass: 342.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H18N2O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: Tris-HCl, PEG-8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.27→42.1 Å / Num. obs: 86073 / % possible obs: 100 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.4
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.84 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GGG

5ggg


Resolution: 1.27→42.124 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1606 2000 2.33 %
Rwork0.1448 --
obs0.1451 85979 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.27→42.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 48 313 2665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122405
X-RAY DIFFRACTIONf_angle_d1.2843268
X-RAY DIFFRACTIONf_dihedral_angle_d17.082865
X-RAY DIFFRACTIONf_chiral_restr0.112377
X-RAY DIFFRACTIONf_plane_restr0.009413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.30180.2791410.2525929X-RAY DIFFRACTION100
1.3018-1.3370.24821410.22575919X-RAY DIFFRACTION100
1.337-1.37630.24061410.19985935X-RAY DIFFRACTION100
1.3763-1.42080.17111410.18165895X-RAY DIFFRACTION100
1.4208-1.47150.18341420.16475970X-RAY DIFFRACTION100
1.4715-1.53050.14881410.13565941X-RAY DIFFRACTION100
1.5305-1.60010.19271420.12875955X-RAY DIFFRACTION100
1.6001-1.68450.1541420.12225952X-RAY DIFFRACTION100
1.6845-1.790.16021430.12655986X-RAY DIFFRACTION100
1.79-1.92820.16421420.13235998X-RAY DIFFRACTION100
1.9282-2.12230.13531440.12836016X-RAY DIFFRACTION100
2.1223-2.42930.16671440.13696055X-RAY DIFFRACTION100
2.4293-3.06060.16141450.15126086X-RAY DIFFRACTION100
3.0606-42.14680.14571510.14486342X-RAY DIFFRACTION100

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