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- PDB-5nr9: A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (alph... -

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Basic information

Entry
Database: PDB / ID: 5nr9
TitleA Native Ternary Complex of Alpha-1,3-Galactosyltransferase (alpha-3GalT) Supports a Conserved Reaction Mechanism for Retaining Glycosyltransferases - Unliganded alpha-3GalT
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
N-acetyllactosaminide alpha-1,3-galactosyltransferase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)69,0075
Polymers68,7312
Non-polymers2763
Water12,556697
1
A: N-acetyllactosaminide alpha-1,3-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4582
Polymers34,3651
Non-polymers921
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)34,5503
Polymers34,3651
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.947, 66.293, 83.933
Angle α, β, γ (deg.)90.00, 102.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-784-

HOH

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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: CATALYTIC DOMAIN, 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.67 Å3/Da / Density % sol: 53.86 % / 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: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 24, 2017
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.7→81.91 Å / Num. obs: 79440 / % possible obs: 100 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0809 / Net I/σ(I): 10.11
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.9901 / Num. unique obs: 7832 / CC1/2: 0.424 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O7Q

1o7q


Resolution: 1.7→81.91 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.31
RfactorNum. reflection% reflection
Rfree0.2234 7425 5.01 %
Rwork0.1872 --
obs0.189 79319 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→81.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4542 0 18 697 5257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124751
X-RAY DIFFRACTIONf_angle_d1.0356454
X-RAY DIFFRACTIONf_dihedral_angle_d13.5052765
X-RAY DIFFRACTIONf_chiral_restr0.063678
X-RAY DIFFRACTIONf_plane_restr0.007815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.38792250.35144567X-RAY DIFFRACTION93
1.7193-1.73960.33322600.33324584X-RAY DIFFRACTION92
1.7396-1.76080.37422600.32594612X-RAY DIFFRACTION94
1.7608-1.78310.35642570.32064663X-RAY DIFFRACTION94
1.7831-1.80650.33972420.31784654X-RAY DIFFRACTION94
1.8065-1.83130.31112760.28864600X-RAY DIFFRACTION94
1.8313-1.85740.32982510.28374585X-RAY DIFFRACTION94
1.8574-1.88520.30092700.27384652X-RAY DIFFRACTION94
1.8852-1.91460.2732350.27484630X-RAY DIFFRACTION94
1.9146-1.9460.27832580.25884654X-RAY DIFFRACTION93
1.946-1.97960.27182510.24214570X-RAY DIFFRACTION93
1.9796-2.01560.2972230.23694585X-RAY DIFFRACTION92
2.0156-2.05430.25052100.22154658X-RAY DIFFRACTION94
2.0543-2.09630.23072310.20894741X-RAY DIFFRACTION94
2.0963-2.14190.22762550.20584667X-RAY DIFFRACTION95
2.1419-2.19170.27362340.20094669X-RAY DIFFRACTION95
2.1917-2.24650.23642350.194737X-RAY DIFFRACTION95
2.2465-2.30730.21292600.17174710X-RAY DIFFRACTION95
2.3073-2.37520.2262510.17864761X-RAY DIFFRACTION95
2.3752-2.45180.21112720.17784720X-RAY DIFFRACTION96
2.4518-2.53950.21692530.17234650X-RAY DIFFRACTION95
2.5395-2.64110.21362480.17424605X-RAY DIFFRACTION94
2.6411-2.76130.2292300.16384809X-RAY DIFFRACTION96
2.7613-2.90690.19342190.16364866X-RAY DIFFRACTION97
2.9069-3.08910.20242370.16274798X-RAY DIFFRACTION97
3.0891-3.32760.20942480.15874788X-RAY DIFFRACTION97
3.3276-3.66250.182500.15114761X-RAY DIFFRACTION96
3.6625-4.19240.20222560.14864751X-RAY DIFFRACTION96
4.1924-5.28190.16022720.13544820X-RAY DIFFRACTION98
5.2819-81.910.20432560.18954808X-RAY DIFFRACTION97

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