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- PDB-5cqn: GTB mutant without mercury - E303C -

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Basic information

Entry
Database: PDB / ID: 5cqn
TitleGTB mutant without mercury - E303C
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / Human ABO(H) blood group system / Glycosyltransferase / Double turn motif / Catalytic domain
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 / : / Golgi cisterna membrane / : / 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 / : / Golgi cisterna membrane / : / 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
Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsGagnon, S.M.L. / Blackler, R.J.
CitationJournal: Glycobiology / Year: 2017
Title: Glycosyltransfer in mutants of putative catalytic residue Glu303 of the human ABO(H) A and B blood group glycosyltransferases GTA and GTB proceeds through a labile active site.
Authors: Blackler, R.J. / Gagnon, S.M. / Polakowski, R. / Rose, N.L. / Zheng, R.B. / Letts, J.A. / Johal, A.R. / Schuman, B. / Borisova, S.N. / Palcic, M.M. / Evans, S.V.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Apr 19, 2017Group: Database references
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Sep 27, 2023Group: 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
X: Histo-blood group ABO system transferase


Theoretical massNumber of molelcules
Total (without water)34,2601
Polymers34,2601
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.570, 149.820, 78.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11X-565-

HOH

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Components

#1: Protein Histo-blood group ABO system transferase / Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N- ...Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-galactosyltransferase / Histo-blood group A transferase / A transferase / Histo-blood group B transferase / B transferase / NAGAT


Mass: 34259.586 Da / Num. of mol.: 1 / Fragment: Catalytic domain (UNP residues 64-354) / Mutation: E303C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Production host: Escherichia coli (E. coli)
References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 30-40 mg/ml protein, 1% PEG (w/v) 4000, 4.5% MPD (v/v), 0.1 M ammonium sulfate, 0.07 M NaCl, 0.05 M ADA buffer, pH 7.5, 5 mM MnCl2 against a reservoir containing 2.7% (w/v) PEG 4000, 7% (v/v) ...Details: 30-40 mg/ml protein, 1% PEG (w/v) 4000, 4.5% MPD (v/v), 0.1 M ammonium sulfate, 0.07 M NaCl, 0.05 M ADA buffer, pH 7.5, 5 mM MnCl2 against a reservoir containing 2.7% (w/v) PEG 4000, 7% (v/v) MPD, 0.32 M ammonium sulfate, 0.25 M NaCl, and 0.2 M ADA pH 7.5

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.61→74.95 Å / Num. obs: 38967 / % possible obs: 96.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.037 / Χ2: 0.96 / Net I/σ(I): 18.5 / Num. measured all: 176577 / Scaling rejects: 1325
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.61-1.673.750.3183.51468738901.218197.4
1.67-1.733.940.26341542238911.178997.7
1.73-1.814.190.1995.11658339211.0814897.4
1.81-1.914.410.1496.81738939061.0516598.2
1.91-2.034.450.119.11771839300.9721497.6
2.03-2.184.620.08911.31836439430.8916198
2.18-2.44.770.0714.21875539140.839297.2
2.4-2.754.850.04721.91898538970.87496.3
2.75-3.464.960.02936.81927538650.8510894.5
3.46-19.565.040.01961.71939938100.8819389.8

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Processing

Software
NameVersionClassification
d*TREK9.4SSIdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
CrystalCleardata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LZ0

1lz0


Resolution: 1.61→74.95 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.551 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 1952 5 %RANDOM
Rwork0.1839 ---
obs0.1851 37011 96.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.92 Å2 / Biso mean: 25.467 Å2 / Biso min: 12.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2--0.35 Å20 Å2
3---0.23 Å2
Refinement stepCycle: final / Resolution: 1.61→74.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 0 190 2403
Biso mean---32.88 -
Num. residues----271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192311
X-RAY DIFFRACTIONr_bond_other_d0.0010.022208
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9523143
X-RAY DIFFRACTIONr_angle_other_deg0.81435062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17122.5108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55915387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2661519
X-RAY DIFFRACTIONr_chiral_restr0.0940.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212586
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02571
X-RAY DIFFRACTIONr_mcbond_it1.6422.3131101
X-RAY DIFFRACTIONr_mcbond_other1.6352.311100
X-RAY DIFFRACTIONr_mcangle_it2.4153.4521378
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 144 -
Rwork0.339 2732 -
all-2876 -
obs--97 %

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