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

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Basic information

Entry
Database: PDB / ID: 5ggk
TitleCrystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Man-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 / reactive gliosis / protein O-linked mannosylation / O-glycan processing / 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 / reactive gliosis / protein O-linked mannosylation / O-glycan processing / acetylglucosaminyltransferase activity / basement membrane organization / dentate gyrus development / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / myelination / sensory perception of sound / gene expression / manganese ion binding / carbohydrate binding / Golgi membrane / membrane
Similarity search - Function
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1, PANDER-like domain / GG-type lectin domain profile. / Glycosyl transferase, family 13 / ILEI/PANDER domain / GNT-I family / Interleukin-like EMT inducer / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
4-nitrophenyl beta-D-mannopyranoside / DI(HYDROXYETHYL)ETHER / Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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)36,35510
Polymers35,2462
Non-polymers1,1098
Water7,710428
1
A: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2336
Polymers17,6231
Non-polymers6105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7480 Å2
MethodPISA
2
B: Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1224
Polymers17,6231
Non-polymers4993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-1 kcal/mol
Surface area7470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.358, 70.129, 89.879
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-622-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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-MBE / 4-nitrophenyl beta-D-mannopyranoside / 4-Nitrophenyl-beta-D-mannopyranoside / 4-nitrophenyl beta-D-mannoside / 4-nitrophenyl D-mannoside / 4-nitrophenyl mannoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO8

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Non-polymers , 4 types, 434 molecules

#3: 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris-HCl, PEG-10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.3→45.8 Å / Num. obs: 83588 / % possible obs: 99.9 % / Redundancy: 12.4 % / Net I/σ(I): 18.9
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.4 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.3→35.065 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1755 2000 2.39 %
Rwork0.1462 --
obs0.1469 83572 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→35.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 75 428 2836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082472
X-RAY DIFFRACTIONf_angle_d1.0473341
X-RAY DIFFRACTIONf_dihedral_angle_d21.058907
X-RAY DIFFRACTIONf_chiral_restr0.095377
X-RAY DIFFRACTIONf_plane_restr0.006420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.33250.27421400.23655737X-RAY DIFFRACTION100
1.3325-1.36850.27251430.22265789X-RAY DIFFRACTION100
1.3685-1.40880.28181410.19855757X-RAY DIFFRACTION100
1.4088-1.45430.24791400.17555734X-RAY DIFFRACTION100
1.4543-1.50630.1961420.15125768X-RAY DIFFRACTION100
1.5063-1.56660.19391410.13735784X-RAY DIFFRACTION100
1.5666-1.63790.1841430.12855801X-RAY DIFFRACTION100
1.6379-1.72420.17741420.11655803X-RAY DIFFRACTION100
1.7242-1.83220.14061420.11615806X-RAY DIFFRACTION100
1.8322-1.97370.16981430.11495819X-RAY DIFFRACTION100
1.9737-2.17230.14481430.11995821X-RAY DIFFRACTION100
2.1723-2.48660.17291430.13655872X-RAY DIFFRACTION100
2.4866-3.13250.18221460.15585934X-RAY DIFFRACTION100
3.1325-35.07720.15771510.15866147X-RAY DIFFRACTION100

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