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

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Basic information

Entry
Database: PDB / ID: 6fwu
TitleCrystal structure of human wild type beta-1,4-galactosyltransferase-1 (B4GalT1) in apo-closed dimeric 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) / Lactose synthesis / Keratan sulfate biosynthesis / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase ...Defective B4GALT1 causes CDG-2d / galactosyltransferase activity / Interaction With Cumulus Cells And The Zona Pellucida / Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) / 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 / Golgi trans cisterna / N-Glycan antennae elongation / penetration of zona pellucida / UDP-galactosyltransferase activity / regulation of acrosome reaction / lactose synthase activity / lactose biosynthetic process / oligosaccharide biosynthetic process / macrophage migration / development of secondary sexual characteristics / desmosome / acute inflammatory response / galactose metabolic process / Pre-NOTCH Processing in Golgi / positive regulation of epithelial cell proliferation involved in wound healing / binding of sperm to zona pellucida / protein N-linked glycosylation / angiogenesis involved in wound healing / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / azurophil granule membrane / epithelial cell development / alpha-tubulin binding / beta-tubulin 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 / Golgi membrane / external side of plasma membrane / Neutrophil degranulation / Golgi apparatus / protein-containing complex / extracellular space / extracellular exosome / identical protein binding / membrane / 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
NITRATE ION / Beta-1,4-galactosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,4-galactosyltransferase 1
B: Beta-1,4-galactosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1304
Polymers63,0062
Non-polymers1242
Water88349
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 area1570 Å2
ΔGint-8 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.217, 60.217, 229.368
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 126 through 145 or (resid 146...
21(chain B and ((resid 126 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPHEPHE(chain A and (resid 126 through 145 or (resid 146...AA126 - 1451 - 20
12ASNASNASNASN(chain A and (resid 126 through 145 or (resid 146...AA14621
13SERSERPROPRO(chain A and (resid 126 through 145 or (resid 146...AA126 - 3971 - 272
14SERSERPROPRO(chain A and (resid 126 through 145 or (resid 146...AA126 - 3971 - 272
15SERSERPROPRO(chain A and (resid 126 through 145 or (resid 146...AA126 - 3971 - 272
16SERSERPROPRO(chain A and (resid 126 through 145 or (resid 146...AA126 - 3971 - 272
21SERSERSERSER(chain B and ((resid 126 and (name N or name...BB1261
22SERSERPROPRO(chain B and ((resid 126 and (name N or name...BB126 - 3971 - 272
23SERSERPROPRO(chain B and ((resid 126 and (name N or name...BB126 - 3971 - 272
24SERSERPROPRO(chain B and ((resid 126 and (name N or name...BB126 - 3971 - 272
25SERSERPROPRO(chain B and ((resid 126 and (name N or name...BB126 - 3971 - 272

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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: 31502.951 Da / Num. of mol.: 2
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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.91 Å3/Da / Density % sol: 35.44 % / Description: 25-100 um triangular prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: 2.35→47.472 Å / Num. obs: 21046 / % possible obs: 99.83 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.3226 / Rpim(I) all: 0.1115 / Rrim(I) all: 0.3418 / Net I/σ(I): 10.48
Reflection shellResolution: 2.35→2.434 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.655 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 2045 / Rpim(I) all: 0.5617 / Rrim(I) all: 1.75 / % possible all: 99.51

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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: 2.35→47.472 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.25
RfactorNum. reflection% reflection
Rfree0.2563 1053 5.01 %
Rwork0.1953 --
obs0.1983 21024 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 273.36 Å2 / Biso mean: 41.9171 Å2 / Biso min: 15.99 Å2
Refinement stepCycle: final / Resolution: 2.35→47.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3998 0 8 50 4056
Biso mean--46.37 30.6 -
Num. residues----504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024117
X-RAY DIFFRACTIONf_angle_d0.5965603
X-RAY DIFFRACTIONf_chiral_restr0.045598
X-RAY DIFFRACTIONf_plane_restr0.003735
X-RAY DIFFRACTIONf_dihedral_angle_d16.5062445
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3023X-RAY DIFFRACTION6.329TORSIONAL
12B3023X-RAY DIFFRACTION6.329TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3502-2.45710.33391280.261824272555
2.4571-2.58670.32171290.254224432572
2.5867-2.74870.30321300.258124692599
2.7487-2.96090.28741290.233124362565
2.9609-3.25880.29241300.222424772607
3.2588-3.73020.29261320.192125132645
3.7302-4.6990.21330.142825232656
4.699-47.48160.20921420.172126832825

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