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- PDB-3i0i: Crystal structure of GTB C80S/C196S/C209S + UDP -

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Basic information

Entry
Database: PDB / ID: 3i0i
TitleCrystal structure of GTB C80S/C196S/C209S + UDP
ComponentsABO glycosyltransferase
KeywordsTRANSFERASE / GTB / glycosyltransferase / ABO Blood group / retaining
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 / hexosyltransferase activity / : / Golgi cisterna membrane / : / antigen 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 / hexosyltransferase activity / : / Golgi cisterna membrane / : / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region / metal ion binding / membrane
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
URIDINE-5'-DIPHOSPHATE / Histo-blood group ABO system transferase / ABO glycosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchuman, B. / Persson, M. / Landry, R.C. / Polakowski, R. / Weadge, J.T. / Seto, N.O.L. / Borisova, S. / Palcic, M.M. / Evans, S.V.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Cysteine-to-serine mutants dramatically reorder the active site of human ABO(H) blood group B glycosyltransferase without affecting activity: structural insights into cooperative substrate binding
Authors: Schuman, B. / Persson, M. / Landry, R.C. / Polakowski, R. / Weadge, J.T. / Seto, N.O. / Borisova, S.N. / Palcic, M.M. / Evans, S.V.
History
DepositionJun 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: ABO glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8092
Polymers33,4051
Non-polymers4041
Water4,089227
1
X: ABO glycosyltransferase
hetero molecules

X: ABO glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6194
Polymers66,8112
Non-polymers8082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4760 Å2
ΔGint-30 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.065, 150.173, 79.770
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 ABO glycosyltransferase


Mass: 33405.320 Da / Num. of mol.: 1 / Fragment: UNP residues 59 to 344 / Mutation: C80S/C196S/C209S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTB / Plasmid: pCW(delta)lac / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q70V26, UniProt: P16442*PLUS, fucosylgalactoside 3-alpha-galactosyltransferase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT GLU 355 IS THE BIOLOGICAL C-TEMINUS

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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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 279.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35mM sodium acetate pH 4.6, 45 mM ADA, 30mM sodium chloride, 3-4 mM magnesium chloride, 3-3.5% PEG 4000, vapor diffusion, hanging drop, temperature 279.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 27, 2005 / Details: Osmic Blue
RadiationMonochromator: Ni FILTER / Protocol: Molecular Replacement / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.49→19.94 Å / Num. obs: 49738 / % possible obs: 96.7 % / Redundancy: 4.35 % / Rmerge(I) obs: 0.035
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible all
1.49-1.543.560.3972.896.7
1.54-1.613.660.3413.297.3
1.61-1.683.80.272497.8
1.68-1.774.020.2025.398.1
1.77-1.884.390.145798.8
1.88-2.024.510.1079.498.8
2.02-2.234.660.07713.198.4
2.23-2.554.810.05818.297.2
2.55-3.214.970.03727.594.9
3.21-19.945.090.01867.389.1

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LZ7

1lz7


Resolution: 1.9→19.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.816 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22574 1213 5.1 %RANDOM
Rwork0.16917 ---
obs0.17196 22739 95.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.772 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 25 227 2468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0222305
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.9593138
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9445270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22723.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19615372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9151516
X-RAY DIFFRACTIONr_chiral_restr0.1690.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211758
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21084
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21554
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2187
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.291.51358
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12322205
X-RAY DIFFRACTIONr_scbond_it3.2273947
X-RAY DIFFRACTIONr_scangle_it5.1494.5933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 78 -
Rwork0.224 1722 -
obs--99.01 %

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