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- PDB-1fg5: CRYSTAL STRUCTURE OF BOVINE ALPHA-1,3-GALACTOSYLTRANSFERASE CATAL... -

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Basic information

Entry
Database: PDB / ID: 1fg5
TitleCRYSTAL STRUCTURE OF BOVINE ALPHA-1,3-GALACTOSYLTRANSFERASE CATALYTIC DOMAIN.
ComponentsN-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE
KeywordsTRANSFERASE / ALPHA BETA ALPHA PROTEIN / NUCLEOTIDE BINDING PROTEIN / ROSSMANN FOLD
Function / homology
Function and homology information


N-acetyllactosaminide 3-alpha-galactosyltransferase / N-acetyllactosaminide 3-alpha-galactosyltransferase activity / Golgi cisterna / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / glycosyltransferase activity / vesicle / carbohydrate metabolic process / Golgi apparatus / metal ion binding
Similarity search - Function
Glycosyl transferase, family 6 / Glycosyltransferase family 6 / 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-acetyllactosaminide alpha-1,3-galactosyltransferase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsGastinel, L.N. / Bignon, C. / Shaper, J.H. / Joziasse, D.H.
CitationJournal: EMBO J. / Year: 2001
Title: Bovine alpha1,3-galactosyltransferase catalytic domain structure and its relationship with ABO histo-blood group and glycosphingolipid glycosyltransferases.
Authors: Gastinel, L.N. / Bignon, C. / Misra, A.K. / Hindsgaul, O. / Shaper, J.H. / Joziasse, D.H.
History
DepositionJul 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)36,9091
Polymers36,9091
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.67, 95.67, 112.93
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE / 13GALT / ALPHA-1 / 3-GALACTOSYLTRANSFERASE


Mass: 36908.566 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Description: CALF THYMUS / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P14769, EC: 2.4.1.151
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.5 Å3/Da / Density % sol: 64.85 % / Description: 0.9796 peak, 0.9800 inflection, 0.9324 remote
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: cacodylate, magnesium chloride, sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlprotein1drop
220 mMTris1drop
32 mM1dropMnCl2
410 mMUMP1drop
5500 mM1dropNaCl
61.3-1.6 Msodium acetate1reservoir
750 mMcacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9796, 0.9800, 0.9324
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Sep 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.981
30.93241
ReflectionResolution: 2.8→36.5 Å / Num. all: 42677 / Num. obs: 11867 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 5.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.12 / % possible all: 95.7
Reflection shell
*PLUS
% possible obs: 95.7 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→36.5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS, Brunger et al
Details: maximum likelihood target using amplitudes and phase probability distribution
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1128 -RANDOM
Rwork0.237 ---
all0.298 42677 --
obs0.28 11867 88.1 %-
Refinement stepCycle: LAST / Resolution: 2.8→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 0 43 2350
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 36.5 Å / σ(F): 0 / Rfactor obs: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

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