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- PDB-6iwq: Crystal structure of GalNAc-T7 with Mn2+ -

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Basic information

Entry
Database: PDB / ID: 6iwq
TitleCrystal structure of GalNAc-T7 with Mn2+
ComponentsN-acetylgalactosaminyltransferase 7
KeywordsTRANSFERASE / Polypeptide N Acetylgalactosaminyltransferase Activity / Transferring Glycosyl Groups / Manganese Ion Binding / Carbohydrate Binding / Metal Ion Binding
Function / homology
Function and homology information


polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / O-linked glycosylation of mucins / protein O-linked glycosylation / carbohydrate binding / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / extracellular exosome ...polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / O-linked glycosylation of mucins / protein O-linked glycosylation / carbohydrate binding / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / extracellular exosome / metal ion binding / membrane
Similarity search - Function
N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A ...N-acetylgalactosaminyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / N-acetylgalactosaminyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsYu, C. / Yin, Y.X.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Structural basis of carbohydrate transfer activity of UDP-GalNAc: Polypeptide N-acetylgalactosaminyltransferase 7.
Authors: Yu, C. / Liang, L. / Yin, Y.
History
DepositionDec 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylgalactosaminyltransferase 7
B: N-acetylgalactosaminyltransferase 7
C: N-acetylgalactosaminyltransferase 7
D: N-acetylgalactosaminyltransferase 7
E: N-acetylgalactosaminyltransferase 7
F: N-acetylgalactosaminyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,51512
Polymers413,1856
Non-polymers3306
Water3,387188
1
A: N-acetylgalactosaminyltransferase 7
C: N-acetylgalactosaminyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8384
Polymers137,7282
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-24 kcal/mol
Surface area46740 Å2
MethodPISA
2
B: N-acetylgalactosaminyltransferase 7
D: N-acetylgalactosaminyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8384
Polymers137,7282
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-21 kcal/mol
Surface area46740 Å2
MethodPISA
3
E: N-acetylgalactosaminyltransferase 7
hetero molecules

F: N-acetylgalactosaminyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8384
Polymers137,7282
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
Buried area1990 Å2
ΔGint-26 kcal/mol
Surface area47080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.695, 158.233, 251.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
N-acetylgalactosaminyltransferase 7 / Polypeptide GalNAc transferase 7 / pp-GaNTase 7 / Protein-UDP acetylgalactosaminyltransferase 7 / ...Polypeptide GalNAc transferase 7 / pp-GaNTase 7 / Protein-UDP acetylgalactosaminyltransferase 7 / UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 7


Mass: 68864.211 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALNT7 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q86SF2, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Lithium sulfate monohydrate, 12%(w/v) Polyethylene glycol 4,000, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 5mM UDP, 5mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→49.25 Å / Num. obs: 103346 / % possible obs: 89 % / Redundancy: 13.1 % / Net I/σ(I): 9.57
Reflection shellResolution: 2.95→3.055 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2400: ???)refinement
DENZOdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→49.25 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.28
RfactorNum. reflection% reflection
Rfree0.2389 5175 5.01 %
Rwork0.2251 --
obs0.2258 103299 88.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.95→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26640 0 6 188 26834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02327444
X-RAY DIFFRACTIONf_angle_d2.00237212
X-RAY DIFFRACTIONf_dihedral_angle_d26.86710254
X-RAY DIFFRACTIONf_chiral_restr0.1043822
X-RAY DIFFRACTIONf_plane_restr0.014800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-2.98360.4284890.34251687X-RAY DIFFRACTION46
2.9836-3.01860.33431200.33262247X-RAY DIFFRACTION62
3.0186-3.05550.30571160.31672407X-RAY DIFFRACTION66
3.0555-3.09410.32731260.31832470X-RAY DIFFRACTION68
3.0941-3.13480.35281280.31192578X-RAY DIFFRACTION70
3.1348-3.17780.32451370.30322645X-RAY DIFFRACTION73
3.1778-3.22320.32791200.29652758X-RAY DIFFRACTION75
3.2232-3.27130.34281540.29312797X-RAY DIFFRACTION77
3.2713-3.32240.34781510.27932913X-RAY DIFFRACTION80
3.3224-3.37680.32531560.283026X-RAY DIFFRACTION82
3.3768-3.4350.27581840.28963106X-RAY DIFFRACTION86
3.435-3.49750.2961630.29153256X-RAY DIFFRACTION89
3.4975-3.56470.28741980.26373414X-RAY DIFFRACTION94
3.5647-3.63750.29311610.25453616X-RAY DIFFRACTION98
3.6375-3.71650.28591940.24813616X-RAY DIFFRACTION99
3.7165-3.8030.24642150.22663605X-RAY DIFFRACTION100
3.803-3.8980.23872010.23283662X-RAY DIFFRACTION100
3.898-4.00340.23241870.21123663X-RAY DIFFRACTION100
4.0034-4.12110.21332200.20443638X-RAY DIFFRACTION100
4.1211-4.25410.1862010.20163677X-RAY DIFFRACTION100
4.2541-4.4060.21192010.18273685X-RAY DIFFRACTION100
4.406-4.58230.19551520.17713717X-RAY DIFFRACTION100
4.5823-4.79070.18812270.17853655X-RAY DIFFRACTION100
4.7907-5.0430.18081950.1833701X-RAY DIFFRACTION100
5.043-5.35860.20191900.19493700X-RAY DIFFRACTION100
5.3586-5.77180.22091970.21253708X-RAY DIFFRACTION100
5.7718-6.35160.24221710.22533767X-RAY DIFFRACTION100
6.3516-7.26810.25012010.21553745X-RAY DIFFRACTION100
7.2681-9.14750.19832070.1893773X-RAY DIFFRACTION100
9.1475-49.2750.19632130.20583892X-RAY DIFFRACTION99

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