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- PDB-2rit: Unliganded B-specific-1,3-galactosyltransferase (GTB) -

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Basic information

Entry
Database: PDB / ID: 2rit
TitleUnliganded B-specific-1,3-galactosyltransferase (GTB)
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 / : / 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
Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 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 12, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,3782
Polymers34,2861
Non-polymers921
Water3,999222
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)68,7554
Polymers68,5712
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5580 Å2
ΔGint-27 kcal/mol
Surface area22600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.535, 149.906, 79.211
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: 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
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: Jun 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.43→20 Å / Num. obs: 57030 / % possible obs: 98.1 % / Redundancy: 4.22 % / Rmerge(I) obs: 0.034 / Χ2: 0.98 / Net I/σ(I): 19.1 / Scaling rejects: 1819
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.43-1.483.210.3223.41796555651.1996.9
1.48-1.543.50.2564.12000056761.1298.5
1.54-1.613.640.20652086856891.0999.2
1.61-1.73.80.16662197857481.0499.5
1.7-1.84.080.137.72370057561.0299.8
1.8-1.944.490.09610.72615357770.9299.7
1.94-2.144.640.068152688357540.8899.3
2.14-2.444.840.04522.52787057310.8798.6
2.44-3.084.940.0335.52835756970.997
3.08-19.85.010.01961.82856956371.0192.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.77 Å19.8 Å
Translation1.77 Å19.8 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
CrystalCleardata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.116 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2887 5.1 %RANDOM
Rwork0.209 ---
obs0.209 57028 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.965 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.43→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 6 222 2515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222383
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.9533234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17122.632114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85915405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1851520
X-RAY DIFFRACTIONr_chiral_restr0.0870.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021810
X-RAY DIFFRACTIONr_nbd_refined0.2050.21148
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21664
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.220
X-RAY DIFFRACTIONr_mcbond_it0.7311.51439
X-RAY DIFFRACTIONr_mcangle_it1.19822300
X-RAY DIFFRACTIONr_scbond_it1.83431069
X-RAY DIFFRACTIONr_scangle_it2.7184.5934
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.611 224 -
Rwork0.558 3869 -
all-4093 -
obs--96.1 %

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