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- PDB-4c2s: Crystal structure of the fucosylgalactoside alpha N- acetylgalact... -

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Basic information

Entry
Database: PDB / ID: 4c2s
TitleCrystal structure of the fucosylgalactoside alpha N- acetylgalactosaminyltransferase (GTA P156L mutant) in complex with UDP and deoxy-H-antigen acceptor
ComponentsHISTO-BLOOD GROUP ABO SYSTEM TRANSFERASE
KeywordsTRANSFERASE / GTA / ABO / BLOOD GROUP ANTIGEN / GLYCOSYLATION
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
: / URIDINE-5'-DIPHOSPHATE / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsWeadge, J.T. / Palcic, M. / Henriksen, A.
CitationJournal: To be Published
Title: Structural and Biochemical Characterization of the Human Blood Group a and B Galactosyltransferases Posessing the Pro156Leu Mutation
Authors: Weadge, J.T. / Palcic, M. / Henriksen, A.
History
DepositionAug 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references / Structure summary
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: HISTO-BLOOD GROUP ABO SYSTEM TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8348
Polymers68,1272
Non-polymers1,7076
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-31.8 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.510, 52.610, 80.270
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number5
Space group name H-MC121

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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: 34063.367 Da / Num. of mol.: 2 / 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
References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-hexyl 3-deoxy-beta-D-galactopyranoside


Type: oligosaccharide / Mass: 394.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2d12h-1b_1-5_1*OCCCCCC][a1221m-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][hexyl]{[(1+1)][b-D-3-deoxy-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsENGINEERED P156L MUTATION AND ENGINEERED EXPRESSION TAG INTRODUCING M63

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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: 2.55 Å3/Da / Density % sol: 51.8 % / Description: NONE
Crystal growpH: 7
Details: 5 MM MOPS PH 7.0, 1 MM MNCL2, 1 MM DTT, 0.1 M AMSO4, 10% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379
DetectorType: MARRESEARCH 165 / Detector: CCD / Date: May 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.938
11h,-k,-l20.062
ReflectionResolution: 2.46→54.5 Å / Num. obs: 21693 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.6
Reflection shellResolution: 2.46→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.2 / % possible all: 78

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y7A

2y7a


Resolution: 2.48→36.88 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.127 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WERE REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18203 1120 5.1 %RANDOM
Rwork0.14503 ---
obs0.14693 20949 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20.31 Å2
2---0.38 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.48→36.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 106 127 4959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194964
X-RAY DIFFRACTIONr_bond_other_d0.0010.024680
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9686744
X-RAY DIFFRACTIONr_angle_other_deg0.876310706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1155579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20922.797236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83515805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9831540
X-RAY DIFFRACTIONr_chiral_restr0.0970.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021223
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_it0.7991.2522321
X-RAY DIFFRACTIONr_mcbond_other0.7991.2522320
X-RAY DIFFRACTIONr_mcangle_it1.2021.8772899
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8471.2632642
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: 2.478→2.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 67 -
Rwork0.152 1438 -
obs--92.62 %

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