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- PDB-5nre: A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a3Ga... -

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Basic information

Entry
Database: PDB / ID: 5nre
TitleA Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a3GalT) Supports a Conserved Reaction Mechanism for Retaining Glycosyltransferases - a3GalT in complex with lactose - a3GalT-LAT
ComponentsN-acetyllactosaminide alpha-1,3-galactosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / GTA
Function / homology
Function and homology information


N-acetyllactosaminide 3-alpha-galactosyltransferase / N-acetyllactosaminide 3-alpha-galactosyltransferase activity / Golgi cisterna / lipid glycosylation / Golgi cisterna membrane / glycosyltransferase activity / protein glycosylation / vesicle / carbohydrate metabolic process / Golgi apparatus / 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
beta-lactose / N-acetyllactosaminide alpha-1,3-galactosyltransferase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsAlbesa-Jove, D. / Marina, A. / Sainz-Polo, M.A. / Guerin, M.E.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Structural Snapshots of alpha-1,3-Galactosyltransferase with Native Substrates: Insight into the Catalytic Mechanism of Retaining Glycosyltransferases.
Authors: Albesa-Jove, D. / Sainz-Polo, M.A. / Marina, A. / Guerin, M.E.
History
DepositionApr 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / struct_conn / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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: N-acetyllactosaminide alpha-1,3-galactosyltransferase
B: N-acetyllactosaminide alpha-1,3-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0733
Polymers68,7312
Non-polymers3421
Water3,549197
1
A: N-acetyllactosaminide alpha-1,3-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7082
Polymers34,3651
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetyllactosaminide alpha-1,3-galactosyltransferase


Theoretical massNumber of molelcules
Total (without water)34,3651
Polymers34,3651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.660, 67.470, 97.890
Angle α, β, γ (deg.)90.00, 119.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein N-acetyllactosaminide alpha-1,3-galactosyltransferase / UDP-galactose:beta-D-galactosyl-1 / 4-N-acetyl-D-glucosaminide alpha-1 / 3-galactosyltransferase / ...UDP-galactose:beta-D-galactosyl-1 / 4-N-acetyl-D-glucosaminide alpha-1 / 3-galactosyltransferase / Galactosyltransferase


Mass: 34365.492 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 80-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GGTA1 / Production host: Escherichia coli (E. coli)
References: UniProt: P14769, N-acetyllactosaminide 3-alpha-galactosyltransferase
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.010 M beta-lactose, 0.02 M L-Na-glutamate, 0.02 M alanine (racemic), 0.02 M glycine, 0.02 M L-lysine (racemic), 0.02 M serine (racemic), 0.1 M Sodium HEPES-MOPS (acid) mix pH 7.5, 20% (v/v) ...Details: 0.010 M beta-lactose, 0.02 M L-Na-glutamate, 0.02 M alanine (racemic), 0.02 M glycine, 0.02 M L-lysine (racemic), 0.02 M serine (racemic), 0.1 M Sodium HEPES-MOPS (acid) mix pH 7.5, 20% (v/v) glycerol and 10% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.98→42.67 Å / Num. obs: 51440 / % possible obs: 98 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 12.67
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.5436 / Mean I/σ(I) obs: 1.93 / Num. unique obs: 5149 / CC1/2: 0.786 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NR9

5nr9


Resolution: 1.98→57.391 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 4753 5.11 %Random
Rwork0.196 ---
obs0.198 92946 90.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→57.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4495 0 23 197 4715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114668
X-RAY DIFFRACTIONf_angle_d1.056350
X-RAY DIFFRACTIONf_dihedral_angle_d19.91664
X-RAY DIFFRACTIONf_chiral_restr0.062680
X-RAY DIFFRACTIONf_plane_restr0.007798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00250.33341670.29152870X-RAY DIFFRACTION89
2.0025-2.02610.33931710.28552906X-RAY DIFFRACTION90
2.0261-2.05080.29681500.27042928X-RAY DIFFRACTION90
2.0508-2.07670.31321720.26682823X-RAY DIFFRACTION88
2.0767-2.10410.26081430.26652927X-RAY DIFFRACTION91
2.1041-2.13290.30381630.26952892X-RAY DIFFRACTION90
2.1329-2.16340.29162110.25342950X-RAY DIFFRACTION91
2.1634-2.19570.29271600.23842867X-RAY DIFFRACTION91
2.1957-2.230.26191790.23372981X-RAY DIFFRACTION91
2.23-2.26650.3011650.22662857X-RAY DIFFRACTION90
2.2665-2.30560.26411590.2252960X-RAY DIFFRACTION91
2.3056-2.34750.25931280.22222993X-RAY DIFFRACTION92
2.3475-2.39270.27161810.21963034X-RAY DIFFRACTION93
2.3927-2.44150.23221600.22442945X-RAY DIFFRACTION93
2.4415-2.49460.29041870.21422985X-RAY DIFFRACTION92
2.4946-2.55260.261610.20792958X-RAY DIFFRACTION92
2.5526-2.61650.25431590.21442997X-RAY DIFFRACTION92
2.6165-2.68720.27481350.21973005X-RAY DIFFRACTION92
2.6872-2.76630.29821440.21692978X-RAY DIFFRACTION92
2.7663-2.85560.30921620.21382944X-RAY DIFFRACTION91
2.8556-2.95760.30811490.21753022X-RAY DIFFRACTION92
2.9576-3.07610.24011580.21132972X-RAY DIFFRACTION92
3.0761-3.2160.28351440.21213019X-RAY DIFFRACTION92
3.216-3.38560.22251470.19952946X-RAY DIFFRACTION92
3.3856-3.59770.21941320.19212900X-RAY DIFFRACTION90
3.5977-3.87540.19831530.16992920X-RAY DIFFRACTION90
3.8754-4.26530.20571670.15582887X-RAY DIFFRACTION89
4.2653-4.88220.18791670.1422954X-RAY DIFFRACTION91
4.8822-6.14990.16811390.16522896X-RAY DIFFRACTION89
6.1499-57.41550.20781400.19332877X-RAY DIFFRACTION89

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