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- PDB-1fr8: CRYSTAL STRUCTURE OF THE BOVINE BETA 1,4 GALACTOSYLTRANSFERASE (B... -

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Basic information

Entry
Database: PDB / ID: 1fr8
TitleCRYSTAL STRUCTURE OF THE BOVINE BETA 1,4 GALACTOSYLTRANSFERASE (B4GALT1) CATALYTIC DOMAIN COMPLEXED WITH URIDINE DIPHOSPHOGALACTOSE
ComponentsBETA 1,4 GALACTOSYLTRANSFERASE
KeywordsTRANSFERASE / nucleotide binding protein alpha beta alpha fold
Function / homology
Function and homology information


protein galactosylation / 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 ...protein galactosylation / 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 / UDP-galactosyltransferase activity / Golgi trans cisterna / lactose synthase activity / lactose biosynthetic process / oligosaccharide biosynthetic process / desmosome / protein N-linked glycosylation / Neutrophil degranulation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / beta-tubulin binding / alpha-tubulin binding / cytoskeletal protein binding / filopodium / brush border membrane / lipid metabolic process / manganese ion binding / basolateral plasma membrane / external side of plasma membrane / Golgi apparatus / 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
GALACTOSE-URIDINE-5'-DIPHOSPHATE / Beta-1,4-galactosyltransferase 1
Similarity search - Component
Biological speciesBos taurus (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
DepositionSep 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / refine ...pdbx_unobs_or_zero_occ_atoms / refine / reflns / struct_ref_seq_dif / struct_site
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _refine.ls_number_reflns_all ..._pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)67,2784
Polymers66,1462
Non-polymers1,1332
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.72, 161.37, 106.31
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: 33072.824 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (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-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.39 Å3/Da / Density % sol: 63.75 %
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→30 Å / Num. obs: 32664 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.2
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.425 / % possible all: 92.6
Reflection
*PLUS
Num. measured all: 138168
Reflection shell
*PLUS
% possible obs: 94 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.4→30 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
Rfree0.262 1000 3.1 %random
Rwork0.237 ---
all0.24 ---
obs0.24 32664 91.9 %-
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4420 0 50 79 4549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg2.1
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 2.1

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