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- PDB-1lzj: Glycosyltransferase B + UDP + H antigen acceptor -

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Basic information

Entry
Database: PDB / ID: 1lzj
TitleGlycosyltransferase B + UDP + H antigen acceptor
ComponentsGlycosyltransferase B
KeywordsTRANSFERASE / GLYCOPROTEIN / TRANSMEMBRANE / SIGNAL-ANCHOR / BLOOD GROUP ANTIGEN
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: 1.32 Å
AuthorsPatenaude, S.I. / Seto, N.O.L. / Borisova, S.N. / Szpacenko, A. / Marcus, S.L. / Palcic, M.M. / Evans, S.V.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The structural basis for specificity in human ABO(H) blood group biosynthesis.
Authors: Patenaude, S.I. / Seto, N.O. / Borisova, S.N. / Szpacenko, A. / Marcus, S.L. / Palcic, M.M. / Evans, S.V.
History
DepositionJun 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 21, 2022Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6818
Polymers34,0091
Non-polymers1,6727
Water6,990388
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycosyltransferase B
hetero molecules

A: Glycosyltransferase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,36216
Polymers68,0192
Non-polymers3,34414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9570 Å2
ΔGint-243 kcal/mol
Surface area22110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.74, 149.48, 79.53
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Glycosyltransferase B / B-specific alpha 1->3 galactosyltransferase


Mass: 34009.273 Da / Num. of mol.: 1 / Fragment: Catalytic domain (RESIDUES 64-354)
Source method: isolated from a genetically manipulated source
Details: N-terminal truncation / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: GenBank: 4590454, UniProt: P16442*PLUS
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-hexyl beta-D-galactopyranoside


Type: oligosaccharide / Mass: 410.456 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2112h-1b_1-5_1*OCCCCCC][a1221m-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][hexyl]{[(1+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 394 molecules

#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#4: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ADA, manganese chloride, ammonium sulfate, MPD, glycerol, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16-8 mg/mlprotein1drop
270 mMADA1droppH7.5
350 mMsodium acetate1droppH4.6
440 mM1dropNaCl
55-8 mM1dropMnCl2
62.5 %(v/v)MPD1drop
75 %(v/v)glycerol1drop
82 %(w/v)PEG40001drop
90.3-0.5 mM3-chloro-Hg-2-methoxy-propylurea1drop
1050 mMADA1reservoirpH7.5
1110 mM1reservoirMnCl2
12100 mMammonium sulfate1reservoir
135 %(v/v)MPD1reservoir
1410 %(v/v)glycerol1reservoir
158-10 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.15 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. all: 72904 / Num. obs: 72904 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.1 Å2 / Limit h max: 39 / Limit h min: 0 / Limit k max: 113 / Limit k min: 0 / Limit l max: 60 / Limit l min: 0 / Observed criterion F max: 876210.83 / Observed criterion F min: 0.32
Reflection shellResolution: 1.32→1.38 Å / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 4.17

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→20 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 6678 10.1 %Random
Rwork0.184 ---
all0.191 74031 --
obs0.189 65709 --
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 87.3772 Å2 / ksol: 0.398117 e/Å3
Displacement parametersBiso max: 58.77 Å2 / Biso min: 8.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Luzzati d res high-1.32
Refinement stepCycle: LAST / Resolution: 1.32→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 0 58 388 2593
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_torsion_deg24.7
X-RAY DIFFRACTIONx_torsion_impr_deg1.32
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.32-1.380.2878009.90.26673080.019142810888.7
1.38-1.450.2486810.20.2376500.0089196851892.6
1.45-1.540.2358509.70.20678770.0089194872794.9
1.54-1.660.21491010.30.19379660.0079219887696.3
1.66-1.830.20392310.30.18480620.0079214898597.5
1.83-2.090.20191210.10.18581430.0079282905597.6
2.09-2.640.20693110.30.18881180.0079320904997.1
2.64-19.790.20993210.30.20180900.0079578902294.2
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor all: 0.191 / Rfactor obs: 0.189 / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg

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