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- PDB-5nrd: A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a-3G... -

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Basic information

Entry
Database: PDB / ID: 5nrd
TitleA Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a-3GalT) Supports a Conserved Reaction Mechanism for Retaining Glycosyltransferases - alpha-3GalT in complex with Co2+, UDP-Gal and lactose - a3GalT-Co2+-UDP-Gal-LAT-2
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 / : / Golgi cisterna membrane / : / glycosyltransferase activity / 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 / : / GALACTOSE-URIDINE-5'-DIPHOSPHATE / N-acetyllactosaminide alpha-1,3-galactosyltransferase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 / pdbx_struct_conn_angle / 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_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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _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.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.value
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)70,4168
Polymers68,7312
Non-polymers1,6856
Water3,981221
1
A: N-acetyllactosaminide alpha-1,3-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4255
Polymers34,3651
Non-polymers1,0604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetyllactosaminide alpha-1,3-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9913
Polymers34,3651
Non-polymers6252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.414, 65.694, 83.014
Angle α, β, γ (deg.)90.00, 102.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#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 (domestic 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

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Non-polymers , 4 types, 226 molecules

#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.58 Å3/Da / Density % sol: 52.32 % / Description: prisms
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 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: 2.12→57.32 Å / Num. obs: 39807 / % possible obs: 99 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.03
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 3918 / CC1/2: 0.519 / % possible all: 100

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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: 2.12→57.316 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.67
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 1872 4.73 %Random selection
Rwork0.2121 ---
obs0.2138 39692 95.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.12→57.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4533 0 103 221 4857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034811
X-RAY DIFFRACTIONf_angle_d0.5936577
X-RAY DIFFRACTIONf_dihedral_angle_d14.2172790
X-RAY DIFFRACTIONf_chiral_restr0.045708
X-RAY DIFFRACTIONf_plane_restr0.004829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.14910.40491290.36662694X-RAY DIFFRACTION94
2.1491-2.17980.36851270.35262879X-RAY DIFFRACTION94
2.1798-2.21230.34451620.34412753X-RAY DIFFRACTION95
2.2123-2.24690.35011450.32462832X-RAY DIFFRACTION95
2.2469-2.28370.34461620.31192773X-RAY DIFFRACTION95
2.2837-2.32310.36541410.30672822X-RAY DIFFRACTION94
2.3231-2.36530.37481480.30152742X-RAY DIFFRACTION94
2.3653-2.41080.33831430.30172800X-RAY DIFFRACTION94
2.4108-2.460.37241540.29342815X-RAY DIFFRACTION95
2.46-2.51350.30971030.27592855X-RAY DIFFRACTION95
2.5135-2.5720.27471410.2642815X-RAY DIFFRACTION95
2.572-2.63630.27561510.25312846X-RAY DIFFRACTION95
2.6363-2.70760.2651290.23762797X-RAY DIFFRACTION95
2.7076-2.78730.26591690.22542769X-RAY DIFFRACTION94
2.7873-2.87720.27461270.22332816X-RAY DIFFRACTION94
2.8772-2.98010.22191420.22817X-RAY DIFFRACTION94
2.9801-3.09940.25221170.19352881X-RAY DIFFRACTION96
3.0994-3.24040.21691090.1832790X-RAY DIFFRACTION94
3.2404-3.41120.25451400.18062915X-RAY DIFFRACTION97
3.4112-3.62490.1971140.18682888X-RAY DIFFRACTION97
3.6249-3.90470.21361500.17532900X-RAY DIFFRACTION97
3.9047-4.29760.19291690.1542872X-RAY DIFFRACTION98
4.2976-4.91910.1861620.14472865X-RAY DIFFRACTION97
4.9191-6.19640.2241430.17932844X-RAY DIFFRACTION95
6.1964-57.33670.21141300.22837X-RAY DIFFRACTION95

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