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- PDB-5m79: Blood group synthase AAGlyB in complex with UMP and cryoprotected... -

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Basic information

Entry
Database: PDB / ID: 5m79
TitleBlood group synthase AAGlyB in complex with UMP and cryoprotected with glycerol
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: 1.3 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 glycerol
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 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.pdbx_dist_value / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,5028
Polymers34,6541
Non-polymers8487
Water5,945330
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)71,00316
Polymers69,3082
Non-polymers1,69514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area8410 Å2
ΔGint-86 kcal/mol
Surface area23110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.606, 148.717, 79.530
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-782-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 337 molecules

#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


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
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: 0.97857 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: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.3→42.083 Å / Num. obs: 75731 / % possible obs: 98.6 % / Redundancy: 4.2 % / Net I/σ(I): 8.7
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.714 / % possible all: 96.3

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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: 1.3→42.083 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.09
RfactorNum. reflection% reflection
Rfree0.1607 3792 5.01 %
Rwork0.1368 --
obs0.138 75696 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→42.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 50 330 2788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132787
X-RAY DIFFRACTIONf_angle_d1.2413805
X-RAY DIFFRACTIONf_dihedral_angle_d25.691053
X-RAY DIFFRACTIONf_chiral_restr0.092398
X-RAY DIFFRACTIONf_plane_restr0.01495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31650.27111410.25252452X-RAY DIFFRACTION91
1.3165-1.33380.2561280.23772545X-RAY DIFFRACTION95
1.3338-1.35210.25581480.2232613X-RAY DIFFRACTION99
1.3521-1.37140.26071540.21132668X-RAY DIFFRACTION99
1.3714-1.39180.25671310.20662613X-RAY DIFFRACTION99
1.3918-1.41360.22421370.19212656X-RAY DIFFRACTION99
1.4136-1.43680.23381220.20352689X-RAY DIFFRACTION99
1.4368-1.46160.24231290.20062682X-RAY DIFFRACTION99
1.4616-1.48810.2411490.19172624X-RAY DIFFRACTION99
1.4881-1.51680.1761180.15812693X-RAY DIFFRACTION99
1.5168-1.54770.14661440.1222665X-RAY DIFFRACTION100
1.5477-1.58140.17041470.12012666X-RAY DIFFRACTION99
1.5814-1.61820.17521430.11912660X-RAY DIFFRACTION99
1.6182-1.65860.17961450.11412652X-RAY DIFFRACTION99
1.6586-1.70350.14871200.11472698X-RAY DIFFRACTION99
1.7035-1.75360.16011390.11622697X-RAY DIFFRACTION99
1.7536-1.81020.14121380.11122670X-RAY DIFFRACTION99
1.8102-1.87490.13971540.10682672X-RAY DIFFRACTION99
1.8749-1.950.15341300.10732676X-RAY DIFFRACTION99
1.95-2.03870.13321340.11242680X-RAY DIFFRACTION99
2.0387-2.14620.14621650.10952626X-RAY DIFFRACTION99
2.1462-2.28060.1531410.11122707X-RAY DIFFRACTION99
2.2806-2.45670.13641370.12062684X-RAY DIFFRACTION99
2.4567-2.70390.13341700.12262672X-RAY DIFFRACTION99
2.7039-3.09510.15261550.13682694X-RAY DIFFRACTION98
3.0951-3.8990.1461440.13352707X-RAY DIFFRACTION98
3.899-42.10470.14251290.15312843X-RAY DIFFRACTION97

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