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- PDB-1g8o: CRYSTALLOGRAPHIC STRUCTURE OF THE NATIVE BOVINE ALPHA-1,3-GALACTO... -

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Basic information

Entry
Database: PDB / ID: 1g8o
TitleCRYSTALLOGRAPHIC STRUCTURE OF THE NATIVE BOVINE ALPHA-1,3-GALACTOSYLTRANSFERASE CATALYTIC DOMAIN
ComponentsN-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE
KeywordsTRANSFERASE / ALPHA-BETA-ALPHA / UDP BINDING PROTEIN
Function / homology
Function and homology information


N-acetyllactosaminide 3-alpha-galactosyltransferase / N-acetyllactosaminide 3-alpha-galactosyltransferase activity / Golgi cisterna / : / Golgi cisterna membrane / : / 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
: / URIDINE-5'-MONOPHOSPHATE / N-acetyllactosaminide alpha-1,3-galactosyltransferase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGastinel, L.N. / Bigon, C. / Misra, A.K. / Hindsgaul, O. / 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
DepositionNov 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7723
Polymers36,3931
Non-polymers3792
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.558, 95.558, 112.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 36392.727 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GGTA1 / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14769, EC: 2.4.1.151
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.53 Å3/Da / Density % sol: 65.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.3 to 1.6 M Sodium Acetate, 10 mM UMP, 2 mM MnCl2, 500 mM NaCl, 0.1 M cacodylate, pH 6.50, 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: ID14-2 / Wavelength: 0.9324 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 17, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9324 Å / Relative weight: 1
ReflectionResolution: 2.3→29 Å / Num. all: 434477 / Num. obs: 23769 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 7.8 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 29 Å / Num. obs: 31286 / % possible obs: 96.5 % / Num. measured all: 434477
Reflection shell
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model MAD solved at 2.8 Angstroms resolution 1fg5.pdb

1fg5


Resolution: 2.3→2.44 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: bulk solvent modeling, Flat model
RfactorNum. reflection% reflectionSelection details
Rfree0.335 383 -Random
Rwork0.274 ---
all0.209 3495 --
obs0.274 3495 99.7 %-
Displacement parametersBiso mean: 51.9 Å2
Baniso -1Baniso -2Baniso -3
1--8.84 Å20 Å20 Å2
2---8.84 Å20 Å2
3---17.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→2.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 22 130 2527
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d1.17
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.335 383 -
Rwork0.274 --
obs-3495 99 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.21 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 51.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.335 / Rfactor Rwork: 0.274

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