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- PDB-5m7a: Blood group synthase AAGlyB in complex with UMP and cryoprotected... -

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Basic information

Entry
Database: PDB / ID: 5m7a
TitleBlood group synthase AAGlyB in complex with UMP and cryoprotected with PEG 3350
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / blood group synthase / glycosyltransferase / dual-specificity / cis-AB mutant
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 / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / 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 / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / 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
: / URIDINE-5'-MONOPHOSPHATE / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.304 Å
AuthorsRocha, J. / Royant, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-BSV8-0011-02 France
CitationJournal: To be published
Title: Blood group synthase AAGlyB in complex with UMP and cryoprotected with PEG 3350
Authors: Rocha, J. / Batot, G.O. / Palcic, M.M. / Breton, C. / Royant, A.
History
DepositionOct 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1294
Polymers34,6541
Non-polymers4753
Water5,891327
1
A: Histo-blood group ABO system transferase
hetero molecules

A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2588
Polymers69,3082
Non-polymers9506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6790 Å2
ΔGint-61 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.853, 149.684, 79.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-772-

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: 34654.008 Da / Num. of mol.: 1 / Mutation: L266G, G268A
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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MOPS buffer, manganese chloride, ammonium sulfate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.304→42.28 Å / Num. obs: 76234 / % possible obs: 98.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.5
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.773 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZGG

3zgg


Resolution: 1.304→37.421 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.6
RfactorNum. reflection% reflection
Rfree0.1811 3820 5.04 %
Rwork0.1451 --
obs0.1469 75815 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.304→37.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 27 327 2688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182601
X-RAY DIFFRACTIONf_angle_d1.4483556
X-RAY DIFFRACTIONf_dihedral_angle_d25.982972
X-RAY DIFFRACTIONf_chiral_restr0.398378
X-RAY DIFFRACTIONf_plane_restr0.011459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.304-1.32050.2931480.25532657X-RAY DIFFRACTION98
1.3205-1.33790.26511240.22052677X-RAY DIFFRACTION99
1.3379-1.35620.3031380.22332701X-RAY DIFFRACTION100
1.3562-1.37560.37161120.28652527X-RAY DIFFRACTION94
1.3756-1.39610.26681550.19932671X-RAY DIFFRACTION99
1.3961-1.41790.22111610.17582654X-RAY DIFFRACTION100
1.4179-1.44120.27621480.23072643X-RAY DIFFRACTION98
1.4412-1.4660.29891440.24892588X-RAY DIFFRACTION96
1.466-1.49270.26581220.22912556X-RAY DIFFRACTION94
1.4927-1.52140.2181460.19372622X-RAY DIFFRACTION96
1.5214-1.55250.23611430.16832613X-RAY DIFFRACTION98
1.5525-1.58620.17731380.12042711X-RAY DIFFRACTION99
1.5862-1.62310.15651410.1172664X-RAY DIFFRACTION99
1.6231-1.66370.15651440.11152695X-RAY DIFFRACTION100
1.6637-1.70870.15431380.11492713X-RAY DIFFRACTION99
1.7087-1.7590.16531510.11472697X-RAY DIFFRACTION100
1.759-1.81580.16691280.1212717X-RAY DIFFRACTION100
1.8158-1.88060.1661470.1292669X-RAY DIFFRACTION99
1.8806-1.95590.18861190.15522510X-RAY DIFFRACTION92
1.9559-2.0450.14311360.12882720X-RAY DIFFRACTION99
2.045-2.15280.16961540.12812578X-RAY DIFFRACTION96
2.1528-2.28760.17211400.12162645X-RAY DIFFRACTION96
2.2876-2.46420.14091390.12352706X-RAY DIFFRACTION100
2.4642-2.71210.15961690.12892687X-RAY DIFFRACTION98
2.7121-3.10440.18181560.14542725X-RAY DIFFRACTION98
3.1044-3.91060.16891470.13822749X-RAY DIFFRACTION99
3.9106-37.43640.16941320.14372900X-RAY DIFFRACTION99

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