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- PDB-8q8i: AO75L in complex with a synthetic trisaccharide acceptor. -

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Basic information

Entry
Database: PDB / ID: 8q8i
TitleAO75L in complex with a synthetic trisaccharide acceptor.
ComponentsExostosin GT47 domain-containing protein
KeywordsTRANSFERASE / Glycosyltransferase / PBCV-1 / Xylosyltransferase / Glycans / VIRAL PROTEIN
Function / homologymetal ion binding / : / DI(HYDROXYETHYL)ETHER / Exostosin GT47 domain-containing protein
Function and homology information
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsLaugueri, M.E. / Speciale, I. / Gimeno, A. / Sicheng, L. / Poveda, A. / Lowary, T. / Van Etten J, L. / Barbero, J. / De Castro, C. / Tonetti, M. / Rojas A, L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesSEV20160644 Spain
CitationJournal: Protein Sci. / Year: 2024
Title: Unveiling the GT114 family: Structural characterization of A075L, a glycosyltransferase from Paramecium bursaria chlorella virus-1 (PBCV-1).
Authors: Laugieri, M.E. / Speciale, I. / Gimeno, A. / Lin, S. / Byers, B.W. / Poveda, A. / Nunez-Franco, R. / Iturrioz, I. / Moure, M.J. / Jimenez-Oses, G. / Russo-Krauss, I. / Notaro, A. / Van ...Authors: Laugieri, M.E. / Speciale, I. / Gimeno, A. / Lin, S. / Byers, B.W. / Poveda, A. / Nunez-Franco, R. / Iturrioz, I. / Moure, M.J. / Jimenez-Oses, G. / Russo-Krauss, I. / Notaro, A. / Van Etten, J.L. / Lowary, T.L. / Jimenez-Barbero, J. / De Castro, C. / Tonetti, M. / Rojas, A.L.
History
DepositionAug 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exostosin GT47 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,06920
Polymers33,4251
Non-polymers1,64419
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-41 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.579, 50.456, 51.543
Angle α, β, γ (deg.)90.00, 96.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-310-

EDO

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Exostosin GT47 domain-containing protein


Mass: 33425.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Gene: A075L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q89410

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Non-polymers , 8 types, 114 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-O5R / (2~{R},3~{S},4~{S},5~{S},6~{R})-2-[(2~{S},3~{R},4~{R},5~{S},6~{R})-5-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-methyl-6-octoxy-3-oxidanyl-oxan-4-yl]oxy-6-methyl-oxane-3,4,5-triol


Mass: 584.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H48O14 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.1
Details: 0.1M TRIS; 0.1M BICINE, pH 8.1 37.5% Morpheus Precipitant mix4 0.03M CaCl2;0.03M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979181 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979181 Å / Relative weight: 1
ReflectionResolution: 1.769→62.9 Å / Num. obs: 12052 / % possible obs: 85.2 % / Redundancy: 4.9 % / CC1/2: 0.986 / Net I/σ(I): 5.4
Reflection shellResolution: 1.796→2.11 Å / Num. unique obs: 604 / CC1/2: 0.626

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Processing

Software
NameVersionClassification
PHENIX(1.18_3855: ???)refinement
autoPROCdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→62.9 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2706 599 4.97 %
Rwork0.2216 --
obs0.2241 12050 37.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→62.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 103 95 2523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022469
X-RAY DIFFRACTIONf_angle_d0.4683322
X-RAY DIFFRACTIONf_dihedral_angle_d11.831354
X-RAY DIFFRACTIONf_chiral_restr0.042364
X-RAY DIFFRACTIONf_plane_restr0.002412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.950.345260.3134129X-RAY DIFFRACTION2
1.95-2.230.3305390.2684973X-RAY DIFFRACTION13
2.23-2.810.29621840.26043402X-RAY DIFFRACTION45
2.81-62.90.25983700.20686947X-RAY DIFFRACTION91

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