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- PDB-2rj9: B-specific alpha-1,3-galactosyltransferase (GTB) + UDP+ Amino-deo... -

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Basic information

Entry
Database: PDB / ID: 2rj9
TitleB-specific alpha-1,3-galactosyltransferase (GTB) + UDP+ Amino-deoxy-acceptor
ComponentsGlycoprotein-fucosylgalactoside alpha-galactosyltransferase
KeywordsTRANSFERASE / GTB ABO Rossman fold BBBB + UDP + ADA / 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 / : / Golgi cisterna membrane / : / 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 / : / Golgi cisterna membrane / : / 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: 1.69 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)35,1664
Polymers34,2861
Non-polymers8813
Water3,513195
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)70,3328
Polymers68,5712
Non-polymers1,7616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6810 Å2
ΔGint-52 kcal/mol
Surface area22450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.430, 149.930, 78.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 34285.559 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-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
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN CORRESPONDS TO WILD TYPE HISTO-BLOOD GROUP B TRANSFERASE. THE SEQUENCE ...THE SEQUENCE OF THIS PROTEIN CORRESPONDS TO WILD TYPE 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: 45.62 %
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 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→19.83 Å / Num. obs: 34204 / % possible obs: 97 % / Redundancy: 4.71 % / Rmerge(I) obs: 0.044 / Χ2: 0.99 / Net I/σ(I): 16.2 / Scaling rejects: 1218
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.69-1.753.980.3253.51385134411.3598.4
1.75-1.824.220.2741442133791.2798.1
1.82-1.94.560.2015.51579334361.2198.3
1.9-24.650.1576.81604834151.1198.1
2-2.134.760.1218.71632234040.9797.3
2.13-2.294.920.097111677833970.997.3
2.29-2.5250.07314.61711334090.8296.6
2.52-2.895.040.0520.81722733920.8195.9
2.89-3.635.080.03132.61745834220.8295.6
3.63-19.834.90.02447.71729835090.8594.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.96 Å19.83 Å
Translation1.96 Å19.83 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: 1.69→19.83 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.297 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1717 5 %RANDOM
Rwork0.2 ---
obs0.202 34200 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.69→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 53 195 2528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222397
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9843258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65722.793111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7515394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8851518
X-RAY DIFFRACTIONr_chiral_restr0.250.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021790
X-RAY DIFFRACTIONr_nbd_refined0.2140.21137
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21623
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2171
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.29
X-RAY DIFFRACTIONr_mcbond_it0.9931.51433
X-RAY DIFFRACTIONr_mcangle_it1.49722265
X-RAY DIFFRACTIONr_scbond_it2.25931110
X-RAY DIFFRACTIONr_scangle_it3.4024.5990
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.512 119 -
Rwork0.431 2403 -
all-2522 -
obs--98.55 %

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