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- PDB-2wgz: Crystal structure of alpha-1,3 galactosyltransferase (alpha3GT) i... -

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Basic information

Entry
Database: PDB / ID: 2wgz
TitleCrystal structure of alpha-1,3 galactosyltransferase (alpha3GT) in a complex with p-nitrophenyl-beta-galactoside (pNP-beta-Gal)
ComponentsN-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYL TRANSFERASE
KeywordsTRANSFERASE / GALACTOSYLTRANSFERASE / GLYCOPROTEIN / METAL-BINDING / SIGNAL-ANCHOR / ALPHA-1 / MEMBRANE / MANGANESE / SUBSTRATE BINDING / GLYCOSYLTRANSFERASE / TRANSMEMBRANE / GOLGI APPARATUS / ENZYME KINETICS
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
4-nitrophenyl beta-D-galactopyranoside / beta-D-galactopyranose / : / P-NITROPHENOL / URIDINE-5'-DIPHOSPHATE / N-acetyllactosaminide alpha-1,3-galactosyltransferase
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsJamaluddin, H. / Tumbale, P. / Ferns, T.A. / Thiyagarajan, N. / Brew, K. / Acharya, K.R.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal Structure of Alpha-1,3 Galactosyltransferase (Alpha3Gt) in a Complex with P-Nitrophenyl-Beta-Galactoside (Pnpbetagal).
Authors: Jamaluddin, H. / Tumbale, P. / Ferns, T.A. / Thiyagarajan, N. / Brew, K. / Acharya, K.R.
History
DepositionApr 28, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-GALACTOSYL TRANSFERASE
B: N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,58615
Polymers68,4952
Non-polymers2,09113
Water9,890549
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-19.2 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.146, 94.222, 94.465
Angle α, β, γ (deg.)90.00, 99.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYL TRANSFERASE / UDP-GALACTOSE\: BETA-D-GALACTOSYL-1\ / 4-N-ACETYL -D-GLUCOSAMINIDE ALPHA-1\ / 3- ...UDP-GALACTOSE\: BETA-D-GALACTOSYL-1\ / 4-N-ACETYL -D-GLUCOSAMINIDE ALPHA-1\ / 3-GALACTOSYLTRANSFERASE / GALACTOSYLTRANSFERASE / ALPHA-1\ / 3 GALACTOSYLTRANSFERASE


Mass: 34247.359 Da / Num. of mol.: 2 / Fragment: RESIDUES 80-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P14769, EC: 2.4.1.151, N-acetyllactosaminide 3-alpha-galactosyltransferase

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Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-147 / 4-nitrophenyl beta-D-galactopyranoside / 1-O-[P-NITROPHENYL]-BETA-D-GALACTOPYRANOSE / 4-nitrophenyl beta-D-galactoside / 4-nitrophenyl D-galactoside / 4-nitrophenyl galactoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H15NO8
IdentifierTypeProgram
1-O-[P-nitrophenyl]-b-D-galactopyranoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#6: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 560 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.9 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 8
Details: 5% PEG 6000, 0.1M TRIS-HCL, PH 8.0 IN THE PRESENCE OF 10MM MNCL2 AND 10MM UDP

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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 5, 2006 / 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: 2.12→50 Å / Num. obs: 44578 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.4
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.14 / % possible all: 80.7

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Processing

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

1k4v


Resolution: 2.12→25.29 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.665 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20582 1077 2.6 %RANDOM
Rwork0.16865 ---
obs0.16959 40981 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.96 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.12→25.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 130 549 5463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225072
X-RAY DIFFRACTIONr_bond_other_d0.0150.025072
X-RAY DIFFRACTIONr_angle_refined_deg1.0011.966876
X-RAY DIFFRACTIONr_angle_other_deg1.4811.966876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7495576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2324.098244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52515860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6591520
X-RAY DIFFRACTIONr_chiral_restr0.0730.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023822
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1720.22399
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23424
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2476
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3721.52978
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.64924680
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.88532473
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4354.52196
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: 2.118→2.173 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 46 -
Rwork0.189 2491 -
obs--77.66 %

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