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- PDB-8ovs: Crystal structure of YeGT glycosyltransferase with bound UDP -

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Basic information

Entry
Database: PDB / ID: 8ovs
TitleCrystal structure of YeGT glycosyltransferase with bound UDP
ComponentsYeGT glycosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase / effector protein / nucleotide binding protein
Function / homologyACETATE ION / : / : / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.123 Å
AuthorsWirth, C. / Hunte, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC 746 Germany
German Federal Ministry for Education and ResearchEXC-2189 Germany
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Tyrosine-modifying glycosylation by Yersinia effectors.
Authors: Schneider, S. / Wirth, C. / Jank, T. / Hunte, C. / Aktories, K.
History
DepositionApr 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: YeGT glycosyltransferase
BBB: YeGT glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,73241
Polymers67,9182
Non-polymers3,81439
Water15,691871
1
AAA: YeGT glycosyltransferase
hetero molecules


  • defined by author
  • Evidence: gel filtration, gel filtration experiment suggest YeGT is monomeric in solution
  • 36 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)35,95121
Polymers33,9591
Non-polymers1,99320
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: YeGT glycosyltransferase
hetero molecules


  • defined by author
  • 35.8 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)35,78020
Polymers33,9591
Non-polymers1,82219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.130, 114.546, 69.376
Angle α, β, γ (deg.)90.000, 89.987, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein YeGT glycosyltransferase


Mass: 33958.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: Y2wildboar1B / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 7 types, 910 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cd
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 871 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES pH 7.5, 500mM sodium acetate, 50mM cadmium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5343
pseudo-merohedral22-h,-k,l20.4657
ReflectionResolution: 1.12→47.13 Å / Num. obs: 213705 / % possible obs: 92.7 % / Redundancy: 30.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.023 / Net I/σ(I): 18
Reflection shellResolution: 1.12→1.22 Å / Redundancy: 18.4 % / Rmerge(I) obs: 2.038 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 10686 / CC1/2: 0.39 / Rpim(I) all: 0.479

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MxCuBEdata collection
autoPROCdata processing
PHASERphasing
STARANISOdata scaling
Cootmodel building
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.123→47.13 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.797 / SU ML: 0.018 / Cross valid method: FREE R-VALUE / ESU R: 0.008 / ESU R Free: 0.007
Details: Hydrogens have been added in their riding positions during refinement. Twin refinement was used with a twin fraction of 0.466 for -h, -k, l as determined by Refmac.
RfactorNum. reflection% reflection
Rfree0.1685 10763 5.037 %
Rwork0.1533 202936 -
all0.154 --
obs-213699 76.61 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.643 Å2
Baniso -1Baniso -2Baniso -3
1--8.967 Å2-0 Å2-0.612 Å2
2--13.568 Å20 Å2
3----4.601 Å2
Refinement stepCycle: LAST / Resolution: 1.123→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4369 0 132 871 5372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134816
X-RAY DIFFRACTIONr_bond_other_d0.010.0164560
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.6546401
X-RAY DIFFRACTIONr_angle_other_deg1.2311.58910517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6785593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98223.167240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.23815843
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg18.238154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.081525
X-RAY DIFFRACTIONr_chiral_restr0.0550.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025437
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021095
X-RAY DIFFRACTIONr_nbd_refined0.1840.2975
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.24193
X-RAY DIFFRACTIONr_nbtor_refined0.1590.22310
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2673
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.219
X-RAY DIFFRACTIONr_nbd_other0.120.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0940.230
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0580.21
X-RAY DIFFRACTIONr_mcbond_it0.8321.6452287
X-RAY DIFFRACTIONr_mcbond_other0.8291.6452285
X-RAY DIFFRACTIONr_mcangle_it1.1572.4722878
X-RAY DIFFRACTIONr_mcangle_other1.1562.4722879
X-RAY DIFFRACTIONr_scbond_it1.0361.82529
X-RAY DIFFRACTIONr_scbond_other0.961.7882487
X-RAY DIFFRACTIONr_scangle_it1.1462.613514
X-RAY DIFFRACTIONr_scangle_other1.1462.613515
X-RAY DIFFRACTIONr_lrange_it2.74822.0195837
X-RAY DIFFRACTIONr_lrange_other2.04620.4355546
X-RAY DIFFRACTIONr_rigid_bond_restr0.71439376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.123-1.1520.705610.791238X-RAY DIFFRACTION6.3089
1.152-1.1840.5321430.62930X-RAY DIFFRACTION15.316
1.184-1.2180.6433250.5095689X-RAY DIFFRACTION30.8142
1.218-1.2560.4495530.4129757X-RAY DIFFRACTION54.3432
1.256-1.2970.3146470.29713038X-RAY DIFFRACTION74.6509
1.297-1.3420.2878050.24615291X-RAY DIFFRACTION90.3001
1.342-1.3930.2498650.21416045X-RAY DIFFRACTION98.3368
1.393-1.450.1968150.17915566X-RAY DIFFRACTION99.4294
1.45-1.5140.1678290.13915025X-RAY DIFFRACTION99.8614
1.514-1.5880.147580.12514368X-RAY DIFFRACTION99.9537
1.588-1.6740.1476790.12913754X-RAY DIFFRACTION99.9723
1.674-1.7750.1516810.1312910X-RAY DIFFRACTION100.0221
1.775-1.8980.1516210.13612222X-RAY DIFFRACTION99.9844
1.898-2.050.1576160.13911348X-RAY DIFFRACTION99.9499
2.05-2.2450.1455700.13610418X-RAY DIFFRACTION100.0091
2.245-2.510.1445190.1399384X-RAY DIFFRACTION99.9899
2.51-2.8970.1554580.1478355X-RAY DIFFRACTION99.9887
2.897-3.5470.1673440.1447073X-RAY DIFFRACTION100.0135
3.547-5.010.1362870.1295486X-RAY DIFFRACTION99.9827
5.01-47.130.1731870.163039X-RAY DIFFRACTION99.9071

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