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- PDB-6fwt: Crystal structure of human wild type beta-1,4-galactosyltransfera... -

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Basic information

Entry
Database: PDB / ID: 6fwt
TitleCrystal structure of human wild type beta-1,4-galactosyltransferase-1 (B4GalT1) in apo-open monomeric form
ComponentsBeta-1,4-galactosyltransferase 1
KeywordsTRANSFERASE / Galactosyltransferase / beta-1 / 4-galactosyltransferase I / B4GalT1 / GalT1 / glycosyltransferase / N-linked glycosylation / apo / monomer / monomeric / open conformation
Function / homology
Function and homology information


Defective B4GALT1 causes CDG-2d / galactosyltransferase activity / Interaction With Cumulus Cells And The Zona Pellucida / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / regulation of acrosome reaction / penetration of zona pellucida / Lactose synthesis / Keratan sulfate biosynthesis / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase ...Defective B4GALT1 causes CDG-2d / galactosyltransferase activity / Interaction With Cumulus Cells And The Zona Pellucida / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / regulation of acrosome reaction / penetration of zona pellucida / Lactose synthesis / Keratan sulfate biosynthesis / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase / N-acetyllactosamine synthase activity / positive regulation of circulating fibrinogen levels / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / N-Glycan antennae elongation / UDP-galactosyltransferase activity / Golgi trans cisterna / macrophage migration / lactose synthase activity / development of secondary sexual characteristics / lactose biosynthetic process / oligosaccharide biosynthetic process / desmosome / galactose metabolic process / acute inflammatory response / positive regulation of epithelial cell proliferation involved in wound healing / Pre-NOTCH Processing in Golgi / binding of sperm to zona pellucida / angiogenesis involved in wound healing / protein N-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / azurophil granule membrane / Golgi cisterna membrane / beta-tubulin binding / epithelial cell development / alpha-tubulin binding / cytoskeletal protein binding / extracellular matrix organization / secretory granule membrane / epithelial cell proliferation / filopodium / brush border membrane / lipid metabolic process / negative regulation of epithelial cell proliferation / manganese ion binding / basolateral plasma membrane / cell adhesion / positive regulation of apoptotic process / external side of plasma membrane / Golgi membrane / Neutrophil degranulation / Golgi apparatus / protein-containing complex / extracellular space / extracellular exosome / membrane / identical protein binding / plasma membrane
Similarity search - Function
Beta-1,4-galactosyltransferase / Galactosyltransferase, N-terminal / N-terminal region of glycosyl transferase group 7 / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / 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
Beta-1,4-galactosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.845 Å
AuthorsHarrus, D. / Kellokumpu, S. / Glumoff, T.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland285232 Finland
CitationJournal: PLoS ONE / Year: 2018
Title: The dimeric structure of wild-type human glycosyltransferase B4GalT1.
Authors: Harrus, D. / Khoder-Agha, F. / Peltoniemi, M. / Hassinen, A. / Ruddock, L. / Kellokumpu, S. / Glumoff, T.
History
DepositionMar 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9812
Polymers31,8891
Non-polymers921
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The gel filtration profile revealed a major peak and a minor peak, corresponding to the size of monomers and dimers, respectively.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-0 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.278, 43.716, 144.348
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Beta-1,4-galactosyltransferase 1 / b4Gal-T1 / UDP-Gal:beta-GlcNAc beta-1 / 4-galactosyltransferase 1 / UDP-galactose:beta-N- ...b4Gal-T1 / UDP-Gal:beta-GlcNAc beta-1 / 4-galactosyltransferase 1 / UDP-galactose:beta-N-acetylglucosamine beta-1


Mass: 31889.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B4GALT1, GGTB2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P15291, Transferases; Glycosyltransferases; Hexosyltransferases, lactose synthase, N-acetyllactosamine synthase, beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.09 Å3/Da / Density % sol: 41.19 % / Description: 50-200 um sticks
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium Nitrate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.845→42.28 Å / Num. obs: 23816 / % possible obs: 99.84 % / Redundancy: 6 % / Rmerge(I) obs: 0.1101 / Rpim(I) all: 0.0483 / Rrim(I) all: 0.1205 / Net I/σ(I): 11.47
Reflection shellResolution: 1.845→1.911 Å / Rmerge(I) obs: 0.9667 / Rpim(I) all: 0.5683 / Rrim(I) all: 1.126

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EE3

4ee3


Resolution: 1.845→42.278 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.55
RfactorNum. reflection% reflection
Rfree0.218 1191 5 %
Rwork0.1659 --
obs0.1685 23814 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.11 Å2 / Biso mean: 31.11 Å2 / Biso min: 14.29 Å2
Refinement stepCycle: final / Resolution: 1.845→42.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 14 195 2455
Biso mean--33.1 34.67 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012354
X-RAY DIFFRACTIONf_angle_d1.0123206
X-RAY DIFFRACTIONf_chiral_restr0.058339
X-RAY DIFFRACTIONf_plane_restr0.008423
X-RAY DIFFRACTIONf_dihedral_angle_d16.4391431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8452-1.91910.32831280.26582446257499
1.9191-2.00640.30111310.22524772608100
2.0064-2.11220.28281300.193824742604100
2.1122-2.24460.26771300.176424652595100
2.2446-2.41780.21831310.158624912622100
2.4178-2.66110.22911320.160124992631100
2.6611-3.04610.21641330.164625292662100
3.0461-3.83740.20241340.137825572691100
3.8374-42.28910.17921420.162326852827100

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