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- PDB-4ayj: Molecular structure of a metal-independent bacterial glycosyltran... -

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Basic information

Entry
Database: PDB / ID: 4ayj
TitleMolecular structure of a metal-independent bacterial glycosyltransferase that catalyzes the synthesis of histo-blood group A antigen
ComponentsBOGT - METAL-INDEPENDENT GLYCOSYLTRANSFERASE
KeywordsTRANSFERASE / CATALYSIS
Function / homology
Function and homology information


hexosyltransferase activity / carbohydrate metabolic process / nucleotide binding / membrane / metal ion binding
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
2'-fucosyllactose / Glycosyltransferase family 6
Similarity search - Component
Biological speciesBACTEROIDES OVATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsThiyagarajan, N. / Pham, T.T.K. / Stinson, B. / Sundriyal, A. / Tumbale, P. / Lizotte-Waniewskib, M. / Brewb, K. / Acharya, K.R.
CitationJournal: Sci.Rep. / Year: 2012
Title: Structure of a Metal-Independent Bacterial Glycosyltransferase that Catalyzes the Synthesis of Histo-Blood Group a Antigen
Authors: Thiyagarajan, N. / Pham, T.T.K. / Stinson, B. / Sundriyal, A. / Tumbale, P. / Lizotte-Waniewski, M. / Brew, K. / Acharya, K.R.
History
DepositionJun 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Jan 29, 2014Group: Database references / Structure summary
Revision 1.4Feb 25, 2015Group: Database references
Revision 1.5May 15, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / 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.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BOGT - METAL-INDEPENDENT GLYCOSYLTRANSFERASE
B: BOGT - METAL-INDEPENDENT GLYCOSYLTRANSFERASE
C: BOGT - METAL-INDEPENDENT GLYCOSYLTRANSFERASE
D: BOGT - METAL-INDEPENDENT GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1068
Polymers116,1524
Non-polymers1,9544
Water00
1
A: BOGT - METAL-INDEPENDENT GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5262
Polymers29,0381
Non-polymers4881
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BOGT - METAL-INDEPENDENT GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5262
Polymers29,0381
Non-polymers4881
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BOGT - METAL-INDEPENDENT GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5262
Polymers29,0381
Non-polymers4881
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BOGT - METAL-INDEPENDENT GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5262
Polymers29,0381
Non-polymers4881
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.850, 93.870, 75.510
Angle α, β, γ (deg.)90.00, 93.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BOGT - METAL-INDEPENDENT GLYCOSYLTRANSFERASE


Mass: 29038.057 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-246
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES OVATUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A7LVT2, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase
#2: Polysaccharide
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / 2'-fucosyllactose


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 488.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2'-fucosyllactose
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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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: 2.16 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BOGT6A (4 MG/ML) AND SACCHARIDE (10 MM) WERE INCUBATED OVERNIGHT AT 16 DEG C AND CRYSTALS WERE GROWN IN A WELL SOLUTION CONTAINING 20 % PEG 3350, 0.1 M BIS-TRIS PROPANE, PH 8.5 AND 0.2 M NA/K TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→70.7 Å / Num. obs: 18669 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 47.78 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.6 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AYL

4ayl


Resolution: 3→70.693 Å / SU ML: 0.92 / σ(F): 1.36 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2619 950 5.1 %
Rwork0.1807 --
obs0.185 18641 93.65 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.329 Å2 / ksol: 0.307 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.7734 Å20 Å219.9858 Å2
2---1.9054 Å20 Å2
3---11.7961 Å2
Refinement stepCycle: LAST / Resolution: 3→70.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7807 0 132 0 7939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098202
X-RAY DIFFRACTIONf_angle_d1.42911156
X-RAY DIFFRACTIONf_dihedral_angle_d16.583064
X-RAY DIFFRACTIONf_chiral_restr0.1041179
X-RAY DIFFRACTIONf_plane_restr0.0081399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.15820.37781250.25852513X-RAY DIFFRACTION93
3.1582-3.35610.37741330.24342535X-RAY DIFFRACTION94
3.3561-3.61520.31291270.21732503X-RAY DIFFRACTION94
3.6152-3.97890.2781440.17842527X-RAY DIFFRACTION94
3.9789-4.55460.22781360.13822518X-RAY DIFFRACTION94
4.5546-5.7380.21771260.14842563X-RAY DIFFRACTION94
5.738-70.71220.21131590.16752532X-RAY DIFFRACTION93

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