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- PDB-8oi9: Trichomonas vaginalis riboside hydrolase in complex with 5-methyl... -

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Basic information

Entry
Database: PDB / ID: 8oi9
TitleTrichomonas vaginalis riboside hydrolase in complex with 5-methyluridine
ComponentsInosine-uridine preferring nucleoside hydrolase family protein
KeywordsHYDROLASE / NH-fold / nucleoside hydrolase / riboside hydrolase / nicotinamide riboside
Function / homology
Function and homology information


purine nucleosidase activity / purine nucleoside catabolic process / metal ion binding / cytosol
Similarity search - Function
Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like
Similarity search - Domain/homology
5-methyluridine / NICKEL (II) ION / Inosine-uridine preferring nucleoside hydrolase family protein
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPatrone, M. / Stockman, B.J. / Degano, M.
Funding support Italy, United States, 2items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG25764 Italy
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R15AI128585 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: A riboside hydrolase that salvages both nucleobases and nicotinamide in the auxotrophic parasite Trichomonas vaginalis.
Authors: Patrone, M. / Galasyn, G.S. / Kerin, F. / Nyitray, M.M. / Parkin, D.W. / Stockman, B.J. / Degano, M.
History
DepositionMar 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine-uridine preferring nucleoside hydrolase family protein
B: Inosine-uridine preferring nucleoside hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,51611
Polymers78,4142
Non-polymers1,1029
Water5,405300
1
A: Inosine-uridine preferring nucleoside hydrolase family protein
B: Inosine-uridine preferring nucleoside hydrolase family protein
hetero molecules

A: Inosine-uridine preferring nucleoside hydrolase family protein
B: Inosine-uridine preferring nucleoside hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,03322
Polymers156,8284
Non-polymers2,20518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)92.490, 92.490, 186.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

21A-544-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 346 / Label seq-ID: 1 - 346

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Inosine-uridine preferring nucleoside hydrolase family protein


Mass: 39206.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_092730 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2FTT0

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Non-polymers , 7 types, 309 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-38T / 5-methyluridine


Mass: 258.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PIN / PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) / PIPES / 1,4-PIPERAZINEDIETHANESULFONIC ACID


Mass: 302.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O6S2 / Comment: pH buffer*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 90 mM PIPES pH 7.0, 90 mM MgCl2, 45 mM KCl, 1 mM NiSO4, 14% (w/v) PEG 5000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2021 / Details: Toroidal mirror
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.95→46.288 Å / Num. obs: 59963 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rpim(I) all: 0.059 / Rsym value: 0.213 / Net I/σ(I): 11.5
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4118 / CC1/2: 0.537 / Rpim(I) all: 1.112 / Rsym value: 3.966

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.288 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.189 / WRfactor Rwork: 0.159 / SU B: 8.249 / SU ML: 0.11 / Average fsc free: 0.963 / Average fsc work: 0.969 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.129
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2036 3026 5.052 %
Rwork0.1731 56868 -
all0.175 --
obs-59894 99.985 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.226 Å2
Baniso -1Baniso -2Baniso -3
1--0.743 Å2-0 Å2-0 Å2
2---0.743 Å20 Å2
3---1.487 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5425 0 64 300 5789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125688
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165354
X-RAY DIFFRACTIONr_angle_refined_deg1.0291.6557709
X-RAY DIFFRACTIONr_angle_other_deg0.3591.57612404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.098524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02110977
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg1.824101
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.45110249
X-RAY DIFFRACTIONr_chiral_restr0.0560.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026426
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021215
X-RAY DIFFRACTIONr_nbd_refined0.2030.21117
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.24995
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22756
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22922
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2297
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1070.29
X-RAY DIFFRACTIONr_nbd_other0.1620.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.222
X-RAY DIFFRACTIONr_mcbond_it1.943.7072755
X-RAY DIFFRACTIONr_mcbond_other1.9373.7062753
X-RAY DIFFRACTIONr_mcangle_it2.9558.3133437
X-RAY DIFFRACTIONr_mcangle_other2.9558.3133438
X-RAY DIFFRACTIONr_scbond_it3.0094.1882933
X-RAY DIFFRACTIONr_scbond_other3.0084.1822929
X-RAY DIFFRACTIONr_scangle_it4.8329.364265
X-RAY DIFFRACTIONr_scangle_other4.8339.3494260
X-RAY DIFFRACTIONr_lrange_it6.67131.1096376
X-RAY DIFFRACTIONr_lrange_other6.63430.9946328
X-RAY DIFFRACTIONr_ncsr_local_group_10.080.0511495
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.079620.0501
12AX-RAY DIFFRACTIONLocal ncs0.079620.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.95-2.0010.3351940.30541180.30643120.9010.9181000.291
2.001-2.0550.2742240.27940460.27942700.9440.9371000.259
2.055-2.1150.2482160.24939010.24941170.9540.9511000.223
2.115-2.180.2642060.22638140.22840200.9480.9611000.197
2.18-2.2510.2431970.21436920.21538900.9530.96599.97430.181
2.251-2.330.2151790.19535990.19637780.970.9731000.164
2.33-2.4180.2471820.19334620.19536440.960.9741000.164
2.418-2.5160.2071790.18333370.18435160.9720.9771000.154
2.516-2.6270.2081840.17131870.17333710.9720.9811000.149
2.627-2.7550.1981560.16430830.16632390.9780.9831000.145
2.755-2.9040.1941780.16929090.17130870.9750.9831000.152
2.904-3.0790.21430.16827910.16929340.9760.9821000.152
3.079-3.2910.2051520.15626180.15927700.9730.9841000.146
3.291-3.5530.1751230.15624530.15725760.9810.9851000.148
3.553-3.890.1761260.15122720.15323980.9830.9851000.147
3.89-4.3450.1761050.14220790.14421840.9830.9881000.143
4.345-5.010.201930.13518450.13819380.9780.9891000.14
5.01-6.1180.218700.15916110.16116810.9770.9861000.162
6.118-8.5770.163780.16312570.16313350.9820.9841000.167
8.577-46.2880.197410.27940.28350.9810.9761000.208
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.07410.0053-0.190.88880.0020.7009-0.00780.0818-0.09130.0318-0.00130.10610.031-0.10630.00910.003-0.00290.00240.10930.00380.029724.406938.0945.5687
21.19730.3908-0.31511.8368-0.23990.89220.177-0.02420.49090.21110.03270.3037-0.3259-0.1046-0.20970.20710.08080.14120.05390.00940.281425.976879.51258.9655
Refinement TLS groupSelection: ALL

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