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- PDB-8avq: AO75L in Complex with UDP-Xylose -

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Basic information

Entry
Database: PDB / ID: 8avq
TitleAO75L in Complex with UDP-Xylose
ComponentsAO75L
KeywordsTRANSFERASE / Glycosyltransferase / PBCV-1 / Xylosyltransferase / Glycans / VIRAL PROTEIN
Function / homologymetal ion binding / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / Exostosin GT47 domain-containing protein
Function and homology information
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLaugeri, M.E. / Speciale, I. / Gimeno, A. / Lin, S. / Poveda, A. / Lowary, T. / Van Etten, J.L. / Barbero, J.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 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 27, 2024Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AO75L
B: AO75L
C: AO75L
D: AO75L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,69183
Polymers135,1554
Non-polymers5,53679
Water14,070781
1
A: AO75L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,10318
Polymers33,7891
Non-polymers1,31417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AO75L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,30223
Polymers33,7891
Non-polymers1,51322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AO75L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,17022
Polymers33,7891
Non-polymers1,38221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: AO75L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,11520
Polymers33,7891
Non-polymers1,32719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.285, 130.427, 87.143
Angle α, β, γ (deg.)90.000, 118.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-316-

EDO

21A-316-

EDO

31C-494-

HOH

41D-501-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
AO75L


Mass: 33788.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Gene: A075L / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q89410

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Non-polymers , 7 types, 860 molecules

#2: Chemical
ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-UDX / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-ALPHA-D-XYLOPYRANOSE


Mass: 536.276 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H22N2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#6: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / 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: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→85.9 Å / Num. obs: 169521 / % possible obs: 99.4 % / Redundancy: 3.536 % / Biso Wilson estimate: 43.435 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.105 / Χ2: 0.87 / Net I/σ(I): 10.6 / Num. measured all: 599433
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.123.3681.0491.239124627532270930.4251.24898.4
2.12-2.273.4480.642.218893825898257920.6860.75999.6
2.27-2.453.6890.4453.648875124124240600.8480.52199.7
2.45-2.683.6320.2845.878043422205221450.9320.33299.7
2.68-33.470.1619.746953520110200410.9710.19199.7
3-3.463.5160.08316.876192117681176110.9920.09899.6
3.46-4.243.7250.04827.015556114983149150.9970.05799.5
4.24-5.983.4870.03731.864014811578115120.9980.04399.4
5.98-85.93.6050.03235.8622899642663520.9980.03898.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ASA

8asa


Resolution: 2→85.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.719 / SU ML: 0.127 / SU R Cruickshank DPI: 0.2056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 4312 5 %RANDOM
Rwork0.1956 ---
obs0.1972 81495 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.83 Å2 / Biso mean: 38.184 Å2 / Biso min: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å2-0.21 Å2
2--0.27 Å20 Å2
3---0.58 Å2
Refinement stepCycle: final / Resolution: 2→85.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9390 0 314 781 10485
Biso mean--42.25 45.21 -
Num. residues----1122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0139904
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179062
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.65513394
X-RAY DIFFRACTIONr_angle_other_deg1.0891.57921086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86251125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.76722.878556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.753151692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3271557
X-RAY DIFFRACTIONr_chiral_restr0.0470.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210679
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022108
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 315 -
Rwork0.292 5948 -
all-6263 -
obs--99.22 %

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