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- PDB-5m7c: Blood group synthase AAGlyB in complex with UDP and cryoprotected... -

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Basic information

Entry
Database: PDB / ID: 5m7c
TitleBlood group synthase AAGlyB in complex with UDP 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 / : / 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
: / DI(HYDROXYETHYL)ETHER / URIDINE-5'-DIPHOSPHATE / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 UDP 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 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,63110
Polymers69,3082
Non-polymers1,3238
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-60 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.730, 77.768, 79.995
Angle α, β, γ (deg.)90.00, 109.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2 / 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, 382 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 374 / 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: 44.97 %
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: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.567
11-H, -K, H+L20.433
ReflectionResolution: 1.6→41.94 Å / Num. obs: 79596 / % possible obs: 99.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 7.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZGG

3zgg


Resolution: 1.6→38.88 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 0.935 / SU ML: 0.035 / Cross valid method: FREE R-VALUE / ESU R: 0.017 / ESU R Free: 0.017
RfactorNum. reflection% reflectionSelection details
Rfree0.18006 3805 4.8 %RANDOM
Rwork0.15065 ---
obs0.15207 75759 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.067 Å2
Baniso -1Baniso -2Baniso -3
1--2.48 Å2-0 Å25.17 Å2
2---4.89 Å2-0 Å2
3---7.37 Å2
Refinement stepCycle: 1 / Resolution: 1.6→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 76 374 5266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195223
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9587120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5495624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16622.471255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4215872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7431549
X-RAY DIFFRACTIONr_chiral_restr0.110.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214043
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8941.4592442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3622.1853084
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1871.6212781
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.27120.3068150
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 263 -
Rwork0.179 5405 -
obs--95.97 %

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