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- PDB-3zgg: Crystal structure of the Fucosylgalactoside alpha N- acetylgalact... -

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Basic information

Entry
Database: PDB / ID: 3zgg
TitleCrystal structure of the Fucosylgalactoside alpha N- acetylgalactosaminyltransferase (GTA, cisAB mutant L266G, G268A) in complex with NPE caged UDP-Gal (C222(1) space group)
ComponentsHISTO-BLOOD GROUP ABO SYSTEM TRANSFERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASES / CATALYTIC DOMAIN
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
1-(2-NITROPHENYL)ETHYL UDP-GALACTOSE / : / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJorgensen, R. / Batot, G.O. / Hindsgaul, O. / Tanaka, H. / Perez, S. / Imberty, A. / Breton, C. / Royant, A. / Palcic, M.M.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structures of a Human Blood Group Glycosyltransferase in Complex with a Photo-Activatable Udp-Gal Derivative Reveal Two Different Binding Conformations
Authors: Jorgensen, R. / Batot, G. / Mannerstedt, K. / Imberty, A. / Breton, C. / Hindsgaul, O. / Royant, A. / Palcic, M.M.
#1: Journal: Carbohydr.Res. / Year: 2008
Title: Synthesis and Photolytic Activation of 6''-O-2-Nitrobenzyl Uridine-5'-Diphosphogalactose: A 'Caged' Udp-Gal Derivative.
Authors: Mannerstedt, K. / Hindsgaul, O.
History
DepositionDec 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.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_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.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: HISTO-BLOOD GROUP ABO SYSTEM TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5034
Polymers34,6541
Non-polymers8493
Water2,414134
1
A: HISTO-BLOOD GROUP ABO SYSTEM TRANSFERASE
hetero molecules

A: HISTO-BLOOD GROUP ABO SYSTEM TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0078
Polymers69,3082
Non-polymers1,6996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5700 Å2
ΔGint-39.1 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.687, 150.730, 79.359
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 HISTO-BLOOD GROUP ABO SYSTEM TRANSFERASE / FUCOSYLGLYCOPROTEIN 3-ALPHA-GALACTOSYLTRANSFERASE / FUCOSYLGLYCOPROTEIN ALPHA-N- ...FUCOSYLGLYCOPROTEIN 3-ALPHA-GALACTOSYLTRANSFERASE / FUCOSYLGLYCOPROTEIN ALPHA-N-ACETYLGALACTOSAMINYLTRANSFERASE / GLYCOPROTEIN-FUCOSYLGALACTOSIDE ALPHA-N-ACETYLGALACTOSAMINYLTRANSFERASE / GLYCOPROTEIN-FUCOSYLGALACTOSIDE ALPHA-GALACTOSYLTRANSFERASE / HISTO-BLOOD GROUP A TRANSFERASE / A TRANSFERASE / HISTO-BLOOD GROUP B TRANSFERASE / B TRANSFERASE / NAGAT / FUCOSYLGLYCOPROTEIN ALPHA-N-ACETYLGALACTOSAMINYLTRANSFERASE SOLUBLE FORM


Mass: 34654.008 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR CATALYTIC DOMAIN, RESIDUES 64-354 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD
References: UniProt: P16442, fucosylgalactoside 3-alpha-galactosyltransferase, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase
#2: Chemical ChemComp-IUG / 1-(2-NITROPHENYL)ETHYL UDP-GALACTOSE


Mass: 702.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N3O19P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 7
Details: 7-12% POLYETHYLENE GLYCOL 3350, 0.1 - 0.3 M AMMONIUM SULPHATE, 0.05 M MNCL2, 0.05 M MOPS PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2011 / Details: TOROIDAL MIROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→49.74 Å / Num. obs: 24091 / % possible obs: 95.5 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3 / % possible all: 80.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IOH

3ioh


Resolution: 1.9→42.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.061 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY. ONLY ONE OF THE TWO POSSIBLE CONFORMATIONS OF THE CAGE HAS BEEN MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22615 1232 5.1 %RANDOM
Rwork0.18354 ---
obs0.18565 22844 94.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.317 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 53 134 2415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192352
X-RAY DIFFRACTIONr_bond_other_d0.0010.022213
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9763201
X-RAY DIFFRACTIONr_angle_other_deg0.76935078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.985273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28722.778108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7815377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2811517
X-RAY DIFFRACTIONr_chiral_restr0.0790.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.306 67 -
Rwork0.234 1326 -
obs--75.62 %

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