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- PDB-2rj4: B-specific alpha-1,3-galactosyltransferase \ G176R +UDP+ADA -

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Basic information

Entry
Database: PDB / ID: 2rj4
TitleB-specific alpha-1,3-galactosyltransferase \ G176R +UDP+ADA
ComponentsGlycoprotein-fucosylgalactoside alpha-galactosyltransferase
KeywordsTRANSFERASE / GTB ABO Rossman fold BBBB unliganded / Blood group antigen / Glycoprotein / Glycosyltransferase / Golgi apparatus / Manganese / Membrane / Metal-binding / Secreted / Signal-anchor / Transmembrane
Function / homology
Function and homology information


fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region
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
Chem-AD7 / : / URIDINE-5'-DIPHOSPHATE / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsEvans, S.V. / Alfaro, J.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: ABO(H) blood group A and B glycosyltransferases recognize substrate via specific conformational changes.
Authors: Alfaro, J.A. / Zheng, R.B. / Persson, M. / Letts, J.A. / Polakowski, R. / Bai, Y. / Borisova, S.N. / Seto, N.O. / Lowary, T.L. / Palcic, M.M. / Evans, S.V.
History
DepositionOct 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.pdbx_dist_value / _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_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: Glycoprotein-fucosylgalactoside alpha-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2664
Polymers34,3861
Non-polymers8813
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycoprotein-fucosylgalactoside alpha-galactosyltransferase
hetero molecules

A: Glycoprotein-fucosylgalactoside alpha-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5338
Polymers68,7712
Non-polymers1,7616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6870 Å2
ΔGint-54 kcal/mol
Surface area22620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.480, 149.740, 79.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glycoprotein-fucosylgalactoside alpha-galactosyltransferase / Fucosylglycoprotein 3-alpha- galactosyltransferase / Histo-blood group B transferase / B transferase


Mass: 34385.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Plasmid: PCW DELTA 1AC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21GOLD
References: UniProt: P16442, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-AD7 / octyl 3-amino-3-deoxy-2-O-(2,6-dideoxy-alpha-L-lyxo-hexopyranosyl)-beta-D-galactopyranoside / 2-deoxy-Fuc-3-amino-Gal-H-antigen disaccharide / amino-deoxy-acceptor


Mass: 421.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H39NO8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN CORRESPONDS TO G176R MUTANT OF HISTO-BLOOD GROUP B TRANSFERASE. THE ...THE SEQUENCE OF THIS PROTEIN CORRESPONDS TO G176R MUTANT OF HISTO-BLOOD GROUP B TRANSFERASE. THE SEQUENCE DIFFERENCES WITH UNP ENTRY P16442 CORRESPOND TO THE VARIENTS BETWEEN P16442 AND GROUP B TRANSFERASE, AS INDICATED IN THE DESCRIPTION OF P16442.

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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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.5
Details: PEG4000 Glycerol MgCl NH2SO4, pH 7.5, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.47→19.95 Å / Num. obs: 53049 / % possible obs: 98.6 % / Redundancy: 4.47 % / Rmerge(I) obs: 0.034 / Χ2: 0.94 / Net I/σ(I): 20 / Scaling rejects: 1793
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.47-1.523.640.2893.81891051801.0797.8
1.52-1.583.740.2324.51971252611.0798.4
1.58-1.663.890.1855.52041952321.0498.7
1.66-1.744.10.1457.12185052971.0499.1
1.74-1.854.470.1089.72396453120.9799.6
1.85-1.994.740.0813.32559453430.999.7
1.99-2.24.860.05918.42626653730.8899.9
2.2-2.515.040.04425.22717253590.8599.4
2.51-3.165.10.03234.82747553520.8598.5
3.16-19.955.060.01960.32758653400.8994.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.78 Å19.95 Å
Translation1.78 Å19.95 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→19.95 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.121 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2704 5.1 %RANDOM
Rwork0.206 ---
obs0.207 53048 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2--0.39 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.47→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 53 230 2674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222512
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9763412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97422.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29315415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6631522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021889
X-RAY DIFFRACTIONr_nbd_refined0.2010.21207
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21729
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2200
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.217
X-RAY DIFFRACTIONr_mcbond_it0.7731.51488
X-RAY DIFFRACTIONr_mcangle_it1.20122359
X-RAY DIFFRACTIONr_scbond_it1.731172
X-RAY DIFFRACTIONr_scangle_it2.634.51053
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.559 212 -
Rwork0.504 3596 -
all-3808 -
obs--97.64 %

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