PDB-8oia: Trichomonas vaginalis riboside hydrolase in complex with D-ribose

ID or keywords:

Entry

Database: PDB / ID: 8oia

Title

Trichomonas vaginalis riboside hydrolase in complex with D-ribose

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 /

cytosol
Similarity search - Function

Biological species

Trichomonas vaginalis (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 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	8oia.cif.gz	704.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8oia.ent.gz	444.8 KB	Display	PDB format
PDBx/mmJSON format	8oia.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oi/8oia ftp://data.pdbj.org/pub/pdb/validation_reports/oi/8oia	HTTPS FTP

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Related structure data

Related structure data	8oi7C 8oi9C 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
Experimental dataset #1	Data reference: 10.15151/ESRF-DC-1110614788 / Data set type: diffraction image data

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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

C: Inosine-uridine preferring nucleoside hydrolase family protein

D: Inosine-uridine preferring nucleoside hydrolase family protein

hetero molecules

158 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	116.995, 135.622, 94.075
Angle α, β, γ (deg.)	90.000, 104.691, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 346 / Label seq-ID: 2 - 346

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein

Inosine-uridine preferring nucleoside hydrolase family protein

Mass: 39206.977 Da / Num. of mol.: 4
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

#3: Sugar

ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose /

Ribose

Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₁₀O₅ / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 116 molecules

#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.3 Å³/Da / Density % sol: 46.56 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.85 Details: 200 mM ammonium citrate dibasic pH 4.85, 15% PEG 3300

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 10, 2021
Radiation	Monochromator: Silicon crystal 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873 Å / Relative weight: 1
Reflection	Resolution: 2.2→43.981 Å / Num. obs: 71792 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC_1/2: 0.981 / R_pim(I) all: 0.136 / R_sym value: 0.305 / Net I/σ(I): 5.2
Reflection shell	Resolution: 2.2→2.25 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4593 / CC_1/2: 0.425 / R_pim(I) all: 0.425 / R_sym value: 1.608 / % possible all: 100

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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: 2.3→43.981 Å / Cor.coef. F_o:F_c: 0.915 / Cor.coef. F_o:F_c free: 0.882 / WR_factor R_free: 0.248 / WR_factor R_work: 0.211 / SU B: 23.249 / SU ML: 0.254 / Average fsc free: 0.9453 / Average fsc work: 0.9573 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.271
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2699	3222	5.126 %
R_work	0.234	59632	-
all	0.236	-	-
obs	-	62854	99.87 %

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: 31.968 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.897 Å²	-0 Å²	0.411 Å²
2-	-	-1.078 Å²	0 Å²
3-	-	-	1.548 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→43.981 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10753	0	72	108	10933

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	11189
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	10541
X-RAY DIFFRACTION	r_angle_refined_deg	1.379	1.658	15162
X-RAY DIFFRACTION	r_angle_other_deg	0.464	1.58	24402
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.986	5	1369
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.361	5	48
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.992	10	1907
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.421	10	497
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	1712
X-RAY DIFFRACTION	r_chiral_restr_other	0.039	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	12684
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2408
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	2374
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	10025
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	5504
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	5826
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	336
X-RAY DIFFRACTION	r_metal_ion_refined	0.112	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.256	0.2	32
X-RAY DIFFRACTION	r_nbd_other	0.243	0.2	71
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.465	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	2.145	2.526	5451
X-RAY DIFFRACTION	r_mcbond_other	2.145	2.526	5450
X-RAY DIFFRACTION	r_mcangle_it	3.259	5.669	6803
X-RAY DIFFRACTION	r_mcangle_other	3.259	5.669	6804
X-RAY DIFFRACTION	r_scbond_it	2.541	2.723	5738
X-RAY DIFFRACTION	r_scbond_other	2.54	2.724	5739
X-RAY DIFFRACTION	r_scangle_it	3.931	6.124	8351
X-RAY DIFFRACTION	r_scangle_other	3.931	6.125	8352
X-RAY DIFFRACTION	r_lrange_it	5.875	25.739	48651
X-RAY DIFFRACTION	r_lrange_other	5.875	25.74	48648
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.083	0.05	11293
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.087	0.05	11276
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.053	0.05	11583
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.049	0.05	12238
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.081	0.05	11334
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.085	0.05	11234

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	0.08304	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08304	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08725	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08725	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05282	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.05282	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.04902	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.04902	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.08138	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.08138	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.0849	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.0849	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
2.3-2.36	0.382	236	0.33	4365	0.333	4603	0.89	0.915	99.9566	0.31
2.36-2.424	0.311	233	0.311	4311	0.311	4544	0.926	0.927	100	0.291
2.424-2.494	0.298	242	0.289	4122	0.29	4365	0.933	0.939	99.9771	0.265
2.494-2.571	0.307	215	0.27	4039	0.272	4255	0.926	0.949	99.9765	0.243
2.571-2.655	0.252	200	0.251	3939	0.251	4139	0.957	0.956	100	0.224
2.655-2.747	0.278	194	0.246	3788	0.248	3983	0.948	0.959	99.9749	0.221
2.747-2.851	0.307	190	0.246	3679	0.249	3872	0.942	0.96	99.9225	0.218
2.851-2.967	0.274	200	0.232	3521	0.234	3721	0.951	0.964	100	0.205
2.967-3.098	0.25	208	0.221	3362	0.223	3570	0.956	0.968	100	0.198
3.098-3.248	0.257	172	0.219	3234	0.221	3412	0.957	0.97	99.8242	0.197
3.248-3.423	0.282	187	0.219	3073	0.223	3262	0.951	0.969	99.9387	0.199
3.423-3.629	0.239	162	0.217	2878	0.218	3045	0.962	0.97	99.8358	0.199
3.629-3.878	0.27	147	0.224	2744	0.227	2894	0.954	0.968	99.8963	0.208
3.878-4.186	0.233	125	0.218	2555	0.219	2685	0.968	0.971	99.8138	0.202
4.186-4.581	0.255	102	0.196	2386	0.198	2491	0.96	0.977	99.8796	0.186
4.581-5.115	0.22	119	0.206	2139	0.206	2265	0.973	0.976	99.6909	0.197
5.115-5.893	0.306	108	0.214	1903	0.218	2013	0.95	0.974	99.9006	0.203
5.893-7.185	0.238	64	0.209	1610	0.211	1677	0.963	0.974	99.8211	0.2
7.185-10.029	0.227	75	0.205	1257	0.206	1336	0.969	0.977	99.7006	0.203
10.029-43.981	0.278	42	0.239	715	0.241	782	0.966	0.968	96.8031	0.239

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	1.361	-0.0391	-0.0515	1.5575	-0.3482	0.5056	0.014	0.1284	0.0895	-0.1053	-0.0038	0.0519	-0.063	-0.0753	-0.0102	0.0387	0.0163	0.0263	0.0255	0.0018	0.1032	14.9909	0.0383	20.2443
2	1.108	0.0485	-0.0828	1.5406	0.0938	0.712	0.0438	0.0815	0.0076	-0.0519	-0.0466	0.0922	-0.0528	-0.0473	0.0028	0.0107	0.01	-0.0204	0.0112	-0.0132	0.0838	-12.419	-35.1762	24.031
3	1.1468	-0.1076	-0.0073	1.5362	-0.0668	0.6591	0.0534	0.0979	-0.0255	-0.062	-0.052	-0.099	0.0528	0.0564	-0.0014	0.0194	0.0106	0.0358	0.0142	0.0006	0.1115	46.9958	-25.8584	23.9371
4	1.302	-0.1738	0.0134	1.6667	0.1163	0.4875	0.006	0.1265	-0.0998	-0.1234	-0.0195	-0.0334	0.0477	0.0853	0.0134	0.0301	0.0184	-0.0061	0.0313	-0.0101	0.1183	19.6903	-60.7625	20.5311

Refinement TLS group

Selection: ALL

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