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- PDB-2jco: Crystal structure of wild type alpha-1,3 Galactosyltransferase in... -

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Basic information

Entry
Database: PDB / ID: 2jco
TitleCrystal structure of wild type alpha-1,3 Galactosyltransferase in the absence of ligands
ComponentsN-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYL TRANSFERASE
KeywordsTRANSFERASE / GALACTOSYLTRANSFERASE / TRANSMEMBRANE / GOLGI APPARATUS / ENZYME MECHANISM / GLYCOPROTEIN / METAL-BINDING / SIGNAL-ANCHOR / ALPHA-1 / MEMBRANE / MANGANESE / GLYCOSYLTRANSFERASE / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


N-acetyllactosaminide 3-alpha-galactosyltransferase / N-acetyllactosaminide 3-alpha-galactosyltransferase activity / Golgi cisterna / lipid glycosylation / Golgi cisterna membrane / glycosyltransferase activity / protein glycosylation / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsJamaluddin, H. / Tumbale, P. / Withers, S.G. / Acharya, K.R. / Brew, K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Conformational Changes Induced by Binding Udp-2F-Galactose to Alpha-1,3 Galactosyltransferase-Implications for Catalysis.
Authors: Jamaluddin, H. / Tumbale, P. / Withers, S.G. / Acharya, K.R. / Brew, K.
History
DepositionDec 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,1822
Polymers34,0901
Non-polymers921
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.570, 93.570, 108.417
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-GALACTOSYL TRANSFERASE / GALACTOSYLTRANSFERASE / UDP-GALACTOSE\:BETA-D-GALACTOSYL-1 / 4-N-ACETYL- D-GLUCOSAMINIDE ALPHA-1 / ...GALACTOSYLTRANSFERASE / UDP-GALACTOSE\:BETA-D-GALACTOSYL-1 / 4-N-ACETYL- D-GLUCOSAMINIDE ALPHA-1 / 3-GALACTOSYLTRANSFERASEALPHA-1 / 3 GALACTOSYLTRANSFERASE


Mass: 34090.164 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 80-368
Source method: isolated from a genetically manipulated source
Details: GLYCEROL / Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14769, EC: 2.4.1.151
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE RANGE FOR THIS PROTEIN CONSTRUCT IS FROM 80 TO 368. THE RESIDUE RANGE MODELLED IN THE ...THE RESIDUE RANGE FOR THIS PROTEIN CONSTRUCT IS FROM 80 TO 368. THE RESIDUE RANGE MODELLED IN THE STRUCTURE IS 82-358

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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: 3.49 Å3/Da / Density % sol: 65 %
Crystal growpH: 8
Details: 0.1M TRIS-HCL BUFFER PH 8.0 AND 1.4M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 30, 2005 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 15988 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 18.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 12 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.11 / % possible all: 84.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4V

1k4v


Resolution: 2.57→27.11 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.862 / SU B: 13.647 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ELECTRON DENSITY FOR REGION A 193 TO A 197 IS DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.328 1041 6.7 %RANDOM
Rwork0.263 ---
obs0.268 14566 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.57→27.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 6 31 2337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222372
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.731.9363212
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4565276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.79523.982113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.9615410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.493159
X-RAY DIFFRACTIONr_chiral_restr0.1180.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021799
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.250.21400
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.21630
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8691.51402
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57722244
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51631123
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3714.5968
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.57→2.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.537 66
Rwork0.39 914

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