PDB-8oi7: Trichomonas vaginalis riboside hydrolase

ID or keywords:

Entry

Database: PDB / ID: 8oi7

Title

Trichomonas vaginalis riboside hydrolase

Components

Inosine-uridine preferring nucleoside hydrolase family protein

Keywords

HYDROLASE / 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

Biological species

Trichomonas vaginalis (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Patrone, M. / Stockman, B.J. / Degano, M.

Funding support

Italy,

United States, 2items

Organization	Grant number	Country
Italian Association for Cancer Research	IG25764	Italy
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R15AI128585	United States

Citation

Journal: 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

Deposition	Mar 22, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 2, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8oi7.cif.gz	377.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8oi7.ent.gz	236.6 KB	Display	PDB format
PDBx/mmJSON format	8oi7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8oi7_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	8oi7_full_validation.pdf.gz	1.3 MB	Display
Data in XML	8oi7_validation.xml.gz	29.3 KB	Display
Data in CIF	8oi7_validation.cif.gz	42.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oi/8oi7 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/8oi7	HTTPS FTP

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Related structure data

Related structure data	8oi9C 8oiaC 8oibC 8oicC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Inosine-uridine preferring nucleoside hydrolase family protein

B: Inosine-uridine preferring nucleoside hydrolase family protein

hetero molecules

78.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author
Evidence: gel filtration
158 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.344, 92.344, 185.111
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	95
Space group name H-M	P4₃22

Components on special symmetry positions

ID	Model	Components
1	1	A-519- HOH
2	1	A-528- HOH
3	1	A-678- HOH
4	1	A-706- HOH
5	1	A-718- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 344 / Label seq-ID: 2 - 344

Dom-ID
1
2

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

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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 , 5 types, 366 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-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.12 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2020 / Details: Toroidal mirror
Radiation	Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9724 Å / Relative weight: 1
Reflection	Resolution: 1.85→46.321 Å / Num. obs: 68295 / % possible obs: 98.8 % / Redundancy: 21.5 % / CC_1/2: 0.999 / R_pim(I) all: 0.027 / R_sym value: 0.149 / Net I/σ(I): 15.1
Reflection shell	Resolution: 1.85→1.89 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6037 / CC_1/2: 0.625 / R_pim(I) all: 0.519 / R_sym value: 1.478 / % possible all: 89.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→46.321 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.959 / WR_factor R_free: 0.192 / WR_factor R_work: 0.176 / SU B: 6.94 / SU ML: 0.099 / Average fsc free: 0.9607 / Average fsc work: 0.9658 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2011	3455	5.073 %
R_work	0.1837	64645	-
all	0.185	-	-
obs	-	68100	98.583 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 41.685 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.47 Å²	0 Å²	0 Å²
2-	-	-1.47 Å²	0 Å²
3-	-	-	2.939 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→46.321 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5468	0	26	358	5852

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	5660
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5331
X-RAY DIFFRACTION	r_angle_refined_deg	1.038	1.653	7656
X-RAY DIFFRACTION	r_angle_other_deg	0.358	1.576	12345
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.46	5	694
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.99	5	24
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.557	10	967
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	0.004	10	1
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.026	10	250
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	856
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	6432
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1213
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	1128
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	5038
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	2794
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	2839
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	345
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.056	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.133	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.145	0.2	87
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.171	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	1.736	2.799	2775
X-RAY DIFFRACTION	r_mcbond_other	1.64	2.797	2772
X-RAY DIFFRACTION	r_mcangle_it	2.555	6.279	3458
X-RAY DIFFRACTION	r_mcangle_other	2.556	6.28	3459
X-RAY DIFFRACTION	r_scbond_it	2.261	3.171	2885
X-RAY DIFFRACTION	r_scbond_other	2.261	3.171	2886
X-RAY DIFFRACTION	r_scangle_it	3.721	7.051	4196
X-RAY DIFFRACTION	r_scangle_other	3.72	7.051	4197
X-RAY DIFFRACTION	r_lrange_it	6.224	23.737	6405
X-RAY DIFFRACTION	r_lrange_other	6.173	23.447	6339
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	11418

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09761	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09761	0.05009

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.85-1.898	0.346	210	0.345	4173	0.345	5003	0.892	0.89	87.6074	0.334
1.898-1.95	0.312	218	0.293	4448	0.294	4911	0.916	0.925	95.0112	0.274
1.95-2.006	0.267	259	0.263	4440	0.263	4763	0.938	0.943	98.6563	0.243
2.006-2.068	0.265	226	0.228	4377	0.23	4616	0.949	0.959	99.7184	0.207
2.068-2.136	0.21	224	0.208	4270	0.208	4504	0.968	0.97	99.778	0.191
2.136-2.21	0.245	228	0.201	4113	0.203	4346	0.961	0.973	99.8849	0.185
2.21-2.294	0.222	227	0.191	3983	0.193	4215	0.971	0.977	99.8814	0.178
2.294-2.387	0.191	233	0.177	3794	0.178	4030	0.973	0.98	99.9256	0.164
2.387-2.493	0.221	184	0.177	3740	0.179	3926	0.97	0.98	99.9491	0.165
2.493-2.614	0.2	187	0.182	3547	0.183	3734	0.974	0.98	100	0.171
2.614-2.755	0.212	179	0.185	3369	0.186	3552	0.972	0.979	99.8874	0.176
2.755-2.922	0.208	178	0.182	3197	0.183	3375	0.975	0.98	100	0.176
2.922-3.122	0.202	179	0.179	3008	0.181	3188	0.974	0.98	99.9686	0.176
3.122-3.371	0.202	143	0.177	2829	0.178	2972	0.974	0.98	100	0.175
3.371-3.691	0.188	124	0.179	2659	0.179	2783	0.979	0.981	100	0.18
3.691-4.124	0.146	128	0.154	2369	0.154	2497	0.987	0.985	100	0.16
4.124-4.755	0.152	114	0.137	2124	0.138	2238	0.986	0.989	100	0.145
4.755-5.809	0.175	90	0.159	1848	0.159	1938	0.982	0.986	100	0.166
5.809-8.151	0.179	88	0.182	1446	0.182	1534	0.983	0.98	100	0.191
8.151-46.321	0.248	36	0.194	911	0.196	947	0.968	0.975	100	0.204

Refinement TLS params.

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

ID	L11 (°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)
1	0.7418	0.0476	-0.3197	0.4115	0.0842	0.1884	-0.0371	0.1033	-0.0411	0.0597	0.0259	0.0286	-0.003	-0.0123	0.0112	0.0898	0.0096	0.0036	0.1717	0.0108	0.223	24.8382	38.5166	5.5503
2	0.2009	0.3543	-0.1973	1.4743	-0.4187	0.2195	0.1849	0.0626	0.2882	0.2654	0.1161	0.3512	-0.1523	-0.04	-0.301	0.2072	0.0848	0.2401	0.0438	0.0552	0.4886	26.1651	79.8326	9.0719

Refinement TLS group

Selection: ALL

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