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- PDB-2rj6: B-specific alpha-1,3-galactosyltransferase G176R S235G mutant (AA... -

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Basic information

Entry
Database: PDB / ID: 2rj6
TitleB-specific alpha-1,3-galactosyltransferase G176R S235G mutant (AABB) + H-antigen disaccharide
ComponentsGlycoprotein-fucosylgalactoside alpha-galactosyltransferase
KeywordsTRANSFERASE / AABB+HA / 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-BHE / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.41 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Glycoprotein-fucosylgalactoside alpha-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7942
Polymers34,3561
Non-polymers4391
Water4,270237
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)69,5884
Polymers68,7112
Non-polymers8772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5100 Å2
ΔGint-26 kcal/mol
Surface area22960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.520, 149.060, 79.610
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: 34355.672 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-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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN CORRESPONDS TO G176R S235G MUTANT OF HISTO-BLOOD GROUP B TRANSFERASE. ...THE SEQUENCE OF THIS PROTEIN CORRESPONDS TO G176R S235G 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: 2.27 Å3/Da / Density % sol: 45.76 %
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: May 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.41→20 Å / Num. obs: 58216 / % possible obs: 96.2 % / Redundancy: 4.18 % / Rmerge(I) obs: 0.037 / Χ2: 0.99 / Net I/σ(I): 21.1 / Scaling rejects: 1838
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.41-1.462.940.3153.41490250631.1184.6
1.46-1.523.420.2674.32036959531.199.8
1.52-1.593.540.2325.22126060071.11100
1.59-1.673.720.1976.22229659931.08100
1.67-1.783.950.158.12377560081.0299.9
1.78-1.914.420.08913.32652159740.9499.4
1.91-2.114.70.05520.32811059550.9398.5
2.11-2.414.890.04525.72886958680.9396.6
2.41-3.035.050.02938.22938257520.994
3.03-19.95.060.0262.42956356430.9789.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.66 Å19.9 Å
Translation1.66 Å19.9 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: 1.41→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.044 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2963 5.1 %RANDOM
Rwork0.215 ---
obs0.216 58214 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.384 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.41→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 28 237 2603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222434
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.9593305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.155283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8922.479117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91715403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8011521
X-RAY DIFFRACTIONr_chiral_restr0.0850.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021845
X-RAY DIFFRACTIONr_nbd_refined0.2080.21197
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21701
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.225
X-RAY DIFFRACTIONr_mcbond_it0.7121.51450
X-RAY DIFFRACTIONr_mcangle_it1.15422311
X-RAY DIFFRACTIONr_scbond_it1.67231118
X-RAY DIFFRACTIONr_scangle_it2.5424.5994
LS refinement shellResolution: 1.41→1.446 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.654 198 -
Rwork0.557 3324 -
all-3522 -
obs--79.72 %

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