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- PDB-2rj1: B-specific alpha-1,3-galactosyltransferase (GTB) G176R mutant + U... -

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Basic information

Entry
Database: PDB / ID: 2rj1
TitleB-specific alpha-1,3-galactosyltransferase (GTB) G176R mutant + UDP + H-antigen disaccharide
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-BHE / : / URIDINE-5'-DIPHOSPHATE / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.55 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.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.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)35,3755
Polymers34,3861
Non-polymers9904
Water3,531196
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)70,75110
Polymers68,7712
Non-polymers1,9798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area7500 Å2
ΔGint-56 kcal/mol
Surface area22510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.450, 149.120, 79.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 200 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BHE / octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside / H-antigen acceptor / alpha-L-Fucp-(1,2)-Beta-D-Galp-O(CH2)7CH3


Mass: 438.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H38O10
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


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


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


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.68 %
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 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→19.74 Å / Num. obs: 44381 / % possible obs: 97.1 % / Redundancy: 4.38 % / Rmerge(I) obs: 0.046 / Χ2: 1 / Net I/σ(I): 15.7 / Scaling rejects: 1471
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.55-1.613.70.3323.41570742241.3294.2
1.61-1.673.790.283.81627542741.2294.7
1.67-1.753.930.2134.91710943301.1495.5
1.75-1.844.20.1696.11849743681.1196.3
1.84-1.954.590.1347.82028143811.0497.1
1.95-2.14.630.09810.62073144360.9797.5
2.1-2.314.750.07713.92142944820.9198.4
2.31-2.654.780.05419.22193545640.8399.1
2.65-3.334.780.03528.92201345850.8299.6
3.33-19.744.60.02346.62206747370.8898.7

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
d*TREKdata reduction
RefinementResolution: 1.55→19.74 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.515 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2258 5.1 %RANDOM
Rwork0.204 ---
obs0.205 44380 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.234 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 60 196 2651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222523
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.983428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0845289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01322.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23315415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5031522
X-RAY DIFFRACTIONr_chiral_restr0.0980.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021898
X-RAY DIFFRACTIONr_nbd_refined0.2040.21204
X-RAY DIFFRACTIONr_nbtor_refined0.310.21726
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.29
X-RAY DIFFRACTIONr_mcbond_it0.7621.51491
X-RAY DIFFRACTIONr_mcangle_it1.16522372
X-RAY DIFFRACTIONr_scbond_it1.77731177
X-RAY DIFFRACTIONr_scangle_it2.7354.51056
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.569 152 -
Rwork0.5 2974 -
all-3126 -
obs--93.96 %

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