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- PDB-4kc2: Structure of the blood group glycosyltransferase AAglyB in comple... -

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Basic information

Entry
Database: PDB / ID: 4kc2
TitleStructure of the blood group glycosyltransferase AAglyB in complex with a pyridine inhibitor as a neutral pyrophosphate surrogate
ComponentsFucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form
KeywordsTransferase/Transferase Inhibitor / GTA superfamily / blood group proteins / glycosyltransferase / Fuc-Gal / UDP-Gal / UDP-GalNAc / Transferase-Transferase Inhibitor complex
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 / : / Chem-WS2 / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCuesta-Seijo, J.A. / Wang, S. / Lafont, D. / Vidal, S. / Palcic, M.M.
CitationJournal: Chemistry / Year: 2013
Title: Design of glycosyltransferase inhibitors: pyridine as a pyrophosphate surrogate.
Authors: Wang, S. / Cuesta-Seijo, J.A. / Lafont, D. / Palcic, M.M. / Vidal, S.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Database references / Refinement description
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_database_related.db_name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _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: Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7694
Polymers33,7351
Non-polymers1,0343
Water6,431357
1
A: Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form
hetero molecules

A: Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5388
Polymers67,4702
Non-polymers2,0686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5180 Å2
ΔGint-36 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.880, 149.900, 80.030
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 Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form / Fucosylglycoprotein 3-alpha-galactosyltransferase / Glycoprotein-fucosylgalactoside alpha-N- ...Fucosylglycoprotein 3-alpha-galactosyltransferase / Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-galactosyltransferase / Histo-blood group A transferase / A transferase / Histo-blood group B transferase / B transferase / NAGAT


Mass: 33735.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Production host: Escherichia coli (E. coli)
References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, 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-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-WS2 / 6-(1-beta-D-Galactopyranosyloxymethyl)-N-(5'-deoxyluridine-5'-yl)picolinamide


Mass: 540.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N4O12
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGLY266 AND ALA268 ARE THE CORRECT IDENTITIES AT THIS POSITION. THESE TWO MUTATIONS MAKE THE PROTEIN ...GLY266 AND ALA268 ARE THE CORRECT IDENTITIES AT THIS POSITION. THESE TWO MUTATIONS MAKE THE PROTEIN A HYBRID BETWEEN THE GTA AND GTB BLOOD GROUP PROTEINS

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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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 13% or 15% PEG 3350, 50 mM or 150 mM ammonium sulfate and 50 mM MOPS pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 35437 / Num. obs: 35437 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.846 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 11.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.90.6643.02734129913100
1.9-2.20.2787.05662798956100
2.2-2.50.16611.15382125200100
2.5-30.11815.05342114690100
3-40.06324.99272853801100
4-50.04831.496051365100
5-70.05129.426427931100
7-100.04931.87244437399.7
10-200.04732.96107317999.4
200.0530.361252990.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IOI

3ioi


Resolution: 1.7→42.32 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1892 / WRfactor Rwork: 0.1625 / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.8875 / SU B: 3.71 / SU ML: 0.065 / SU R Cruickshank DPI: 0.107 / SU Rfree: 0.1015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.102 / Stereochemistry target values: Refmac 5 dictionary / Details: U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1064 3 %RANDOM
Rwork0.1763 ---
all0.1772 35436 --
obs0.1772 35436 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 61.85 Å2 / Biso mean: 13.989 Å2 / Biso min: 5.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å20 Å2
2--0.35 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 58 357 2771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022586
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.973532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5585315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16622.64125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58215427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2661523
X-RAY DIFFRACTIONr_chiral_restr0.0780.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211992
X-RAY DIFFRACTIONr_mcbond_it0.4190.8621194
X-RAY DIFFRACTIONr_mcangle_it0.7761.2921504
X-RAY DIFFRACTIONr_scbond_it0.3790.9351391
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 77 -
Rwork0.23 2486 -
all-2563 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: 10.231 Å / Origin y: 20.288 Å / Origin z: -6.154 Å
111213212223313233
T0.0272 Å2-0.0009 Å20.0005 Å2-0.0321 Å20.0001 Å2--0.0298 Å2
L0.273 °20.0284 °20.0328 °2-0.028 °20.0904 °2--0.3117 °2
S0.0363 Å °-0.0297 Å °0.0175 Å °0.0047 Å °-0.0094 Å °-0.0056 Å °0.0168 Å °-0.0109 Å °-0.0269 Å °

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