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- PDB-1fgx: CRYSTAL STRUCTURE OF THE BOVINE BETA 1,4 GALACTOSYLTRANSFERASE (B... -

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Entry
Database: PDB / ID: 1fgx
TitleCRYSTAL STRUCTURE OF THE BOVINE BETA 1,4 GALACTOSYLTRANSFERASE (B4GALT1) CATALYTIC DOMAIN COMPLEXED WITH UMP
ComponentsBETA 1,4 GALACTOSYLTRANSFERASE
KeywordsTRANSFERASE / nucleotide binding protein / alpha beta alpha fold
Function / homology
Function and homology information


: / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / lactose synthase / neolactotriaosylceramide beta-1,4-galactosyltransferase / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase / N-acetyllactosamine synthase / N-acetyllactosamine synthase activity ...: / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / 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 / 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 / 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 / Neutrophil degranulation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / epithelial cell development / alpha-tubulin binding / beta-tubulin binding / extracellular matrix organization / 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 apparatus / protein-containing complex / extracellular space / identical protein binding
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
URIDINE-5'-MONOPHOSPHATE / Beta-1,4-galactosyltransferase 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsGastinel, L.N. / Cambillau, C. / Bourne, Y.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structures of the bovine beta4galactosyltransferase catalytic domain and its complex with uridine diphosphogalactose.
Authors: Gastinel, L.N. / Cambillau, C. / Bourne, Y.
History
DepositionJul 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 21, 2021Group: Data collection / Derived calculations / Refinement description
Category: refine / reflns / struct_site
Item: _refine.ls_number_reflns_all / _refine.ls_percent_reflns_R_free ..._refine.ls_number_reflns_all / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _reflns.number_all / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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

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Assembly

Deposited unit
A: BETA 1,4 GALACTOSYLTRANSFERASE
B: BETA 1,4 GALACTOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4983
Polymers66,1742
Non-polymers3241
Water2,612145
1
A: BETA 1,4 GALACTOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)33,0871
Polymers33,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA 1,4 GALACTOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4112
Polymers33,0871
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.5, 161, 107.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BETA 1,4 GALACTOSYLTRANSFERASE / BETA4GALT1


Mass: 33086.852 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: LIVER / Plasmid: PEE12 / Cell line (production host): NSO / Production host: Mus musculus (house mouse)
References: UniProt: P08037, beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase
#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.54 Å3/Da / Density % sol: 65.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 5000, Tris, MnCl2, Li2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-15 mg/mlprotein1drop
220 mMTris Maleate1drop
32 mM1dropMnCl2
450 mM1dropNaCl
525-30 %PEG50001reservoir
6100-150 mM1reservoirLi2SO4
7100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→29.28 Å / Num. obs: 34096 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 9.2
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.35 / Num. unique all: 5517 / % possible all: 97.4
Reflection
*PLUS
Num. measured all: 91528
Reflection shell
*PLUS
% possible obs: 95 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
DMmodel building
CNS0.9refinement
CCP4(SCALA)data scaling
DMphasing
RefinementResolution: 2.4→29.28 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS / Details: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1026 3 %random
Rwork0.225 ---
obs-34096 96 %-
Refinement stepCycle: LAST / Resolution: 2.4→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4443 0 21 145 4609
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.9
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / σ(F): 0 / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.9

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