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

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Basic information

Entry
Database: PDB / ID: 5ggn
TitleCrystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-beta-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 mannosylation / O-glycan processing / 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 mannosylation / O-glycan processing / 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-LEC / Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.211 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 1.2Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly / pdbx_struct_oper_list / 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 / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 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

Downloads & links

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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
Water10,124562
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
MethodPISA
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
MethodPISA
Unit cell
Length a, b, c (Å)70.524, 90.481, 53.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-690-

HOH

21A-704-

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-LEC / 4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside / N-[(2S,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(4-nitrophenoxy)oxan-3-yl]ethanamide / 4-nitrophenyl 2-acetamido-2-deoxy-beta-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: obtained synthetically / Formula: C14H18N2O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: Tris-HCl, PEG-6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.21→19.441 Å / Num. obs: 200500 / % possible obs: 99.4 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 24.8
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 3 / % possible all: 93.8

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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: 1.211→19.441 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.15
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.1657 3842 1.92 %
Rwork0.1439 --
obs0.1443 200500 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.211→19.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 48 562 2932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152439
X-RAY DIFFRACTIONf_angle_d1.4463312
X-RAY DIFFRACTIONf_dihedral_angle_d19.494872
X-RAY DIFFRACTIONf_chiral_restr0.122378
X-RAY DIFFRACTIONf_plane_restr0.009421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2108-1.22620.28421290.23336570X-RAY DIFFRACTION90
1.2262-1.24230.25941430.20927376X-RAY DIFFRACTION100
1.2423-1.25930.2461450.19057291X-RAY DIFFRACTION100
1.2593-1.27730.19631410.17447355X-RAY DIFFRACTION100
1.2773-1.29640.18891430.17547269X-RAY DIFFRACTION100
1.2964-1.31660.18891440.16137353X-RAY DIFFRACTION100
1.3166-1.33820.18321420.15517354X-RAY DIFFRACTION100
1.3382-1.36130.17711440.15217331X-RAY DIFFRACTION100
1.3613-1.3860.19571420.14777327X-RAY DIFFRACTION100
1.386-1.41260.18671450.14577342X-RAY DIFFRACTION100
1.4126-1.44150.16751470.13647362X-RAY DIFFRACTION100
1.4415-1.47280.15491420.12767298X-RAY DIFFRACTION100
1.4728-1.50710.15231440.12517362X-RAY DIFFRACTION100
1.5071-1.54470.17321420.11927286X-RAY DIFFRACTION100
1.5447-1.58650.1511450.1217362X-RAY DIFFRACTION100
1.5865-1.63310.15151430.11867292X-RAY DIFFRACTION100
1.6331-1.68580.19021470.11947335X-RAY DIFFRACTION100
1.6858-1.7460.14561420.12427347X-RAY DIFFRACTION100
1.746-1.81590.16021410.13557343X-RAY DIFFRACTION100
1.8159-1.89850.1921400.13097323X-RAY DIFFRACTION100
1.8985-1.99850.16661450.12537335X-RAY DIFFRACTION100
1.9985-2.12350.14631460.12967348X-RAY DIFFRACTION100
2.1235-2.28730.14231420.13357322X-RAY DIFFRACTION100
2.2873-2.5170.16811420.14647345X-RAY DIFFRACTION100
2.517-2.88020.1431430.15037316X-RAY DIFFRACTION100
2.8802-3.62490.15121400.14817319X-RAY DIFFRACTION100
3.6249-19.44380.18021330.16276795X-RAY DIFFRACTION93

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