PDB-8oib: Trichomonas vaginalis riboside hydrolase in complex with glycerol

ID or keywords:

Entry

Database: PDB / ID: 8oib

Title

Trichomonas vaginalis riboside hydrolase in complex with glycerol

Components

Inosine-uridine preferring nucleoside hydrolase family protein

Keywords

HYDROLASE / NH-fold / nucleoside hydrolase / riboside hydrolase / nicotinamide riboside

Function / homology

purine nucleosidase activity / Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / purine nucleoside catabolic process / metal ion binding / cytosol / Inosine-uridine preferring nucleoside hydrolase family protein

Function and homology information

Biological species

Trichomonas vaginalis (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.44 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

-
Download

PDBx/mmCIF format	8oib.cif.gz	698.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8oib.ent.gz	442.4 KB	Display	PDB format
PDBx/mmJSON format	8oib.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8oib_validation.pdf.gz	2.6 MB	Display	wwPDB validaton report
Full document	8oib_full_validation.pdf.gz	2.6 MB	Display
Data in XML	8oib_validation.xml.gz	46.9 KB	Display
Data in CIF	8oib_validation.cif.gz	64.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oi/8oib ftp://data.pdbj.org/pub/pdb/validation_reports/oi/8oib	HTTPS FTP

-
Related structure data

Related structure data	8oi7C 8oi9C 8oiaC 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-1110614797 / Data set type: diffraction image data

-
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

157 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)	51.034, 156.998, 88.729
Angle α, β, γ (deg.)	90.000, 90.562, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	GLY	GLY	A	A	2 - 346	2 - 346
2	1	1	SER	SER	GLY	GLY	B	B	2 - 346	2 - 346
3	2	2	SER	SER	GLU	GLU	A	A	2 - 344	2 - 344
4	2	2	SER	SER	GLU	GLU	C	C	2 - 344	2 - 344
5	3	3	SER	SER	ILE	ILE	A	A	2 - 345	2 - 345
6	3	3	SER	SER	ILE	ILE	D	D	2 - 345	2 - 345
7	4	4	MET	MET	GLU	GLU	B	B	1 - 344	1 - 344
8	4	4	MET	MET	GLU	GLU	C	C	1 - 344	1 - 344
9	5	5	SER	SER	LYS	LYS	B	B	2 - 347	2 - 347
10	5	5	SER	SER	LYS	LYS	D	D	2 - 347	2 - 347
11	6	6	SER	SER	GLU	GLU	C	C	2 - 344	2 - 344
12	6	6	SER	SER	GLU	GLU	D	D	2 - 344	2 - 344

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

#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
#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
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.73 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.85 Details: 200 mM ammonium citrate dibasic pH 4.85, 15% w/v PEG 5000 monomethyl ether, 17.5% (v/v) glycerol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 22, 2021
Radiation	Monochromator: Silicon crystal 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.44→88.73 Å / Num. obs: 50817 / % possible obs: 98 % / Redundancy: 3 % / CC_1/2: 0.993 / R_pim(I) all: 0.058 / R_sym value: 0.086 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2.44→2.48 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2518 / CC_1/2: 0.848 / R_pim(I) all: 0.317 / R_sym value: 0.473 / % possible all: 99.2

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.44→88.725 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.941 / WR_factor R_free: 0.25 / WR_factor R_work: 0.205 / SU B: 23.828 / SU ML: 0.24 / Average fsc free: 0.957 / Average fsc work: 0.969 / Cross valid method: THROUGHOUT / ESU R: 0.677 / ESU R Free: 0.266
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2255	2482	4.885 %
R_work	0.1885	48324	-
all	0.19	-	-
obs	-	50806	98.011 %

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: 55.063 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.118 Å²	0 Å²	-0.311 Å²
2-	-	-0.622 Å²	0 Å²
3-	-	-	-2.49 Å²

Refinement step

Cycle: LAST / Resolution: 2.44→88.725 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10610	0	28	120	10758

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	10942
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	10240
X-RAY DIFFRACTION	r_angle_refined_deg	1.179	1.653	14808
X-RAY DIFFRACTION	r_angle_other_deg	0.4	1.576	23693
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.896	5	1334
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.573	5	48
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.75	10	1848
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.573	10	491
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	1656
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	12457
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2367
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	2283
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.185	0.2	10020
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	5415
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	5807
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.174	0.2	300
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.047	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.3	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.213	0.2	37
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.005	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	3.754	4.469	5369
X-RAY DIFFRACTION	r_mcbond_other	3.751	4.468	5367
X-RAY DIFFRACTION	r_mcangle_it	5.763	10.026	6684
X-RAY DIFFRACTION	r_mcangle_other	5.763	10.027	6685
X-RAY DIFFRACTION	r_scbond_it	4.454	4.974	5573
X-RAY DIFFRACTION	r_scbond_other	4.454	4.974	5574
X-RAY DIFFRACTION	r_scangle_it	6.971	11.108	8124
X-RAY DIFFRACTION	r_scangle_other	6.97	11.108	8125
X-RAY DIFFRACTION	r_lrange_it	9.102	38.258	12124
X-RAY DIFFRACTION	r_lrange_other	9.098	38.26	12121
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.068	0.05	11460
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.081	0.05	11106
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.073	0.05	11401
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.08	0.05	11139
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.076	0.05	11375
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.079	0.05	11170

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	0.06784	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.06784	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08091	0.0501
2	4	C	X-RAY DIFFRACTION	Local ncs	0.08091	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07309	0.0501
3	6	D	X-RAY DIFFRACTION	Local ncs	0.07309	0.0501
4	7	B	X-RAY DIFFRACTION	Local ncs	0.08032	0.0501
4	8	C	X-RAY DIFFRACTION	Local ncs	0.08032	0.0501
5	9	B	X-RAY DIFFRACTION	Local ncs	0.07641	0.0501
5	10	D	X-RAY DIFFRACTION	Local ncs	0.07641	0.0501
6	11	C	X-RAY DIFFRACTION	Local ncs	0.07901	0.0501
6	12	D	X-RAY DIFFRACTION	Local ncs	0.07901	0.0501

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
2.44-2.503	0.325	174	0.307	3594	0.308	3805	0.919	0.925	99.0276	0.305
2.503-2.572	0.344	172	0.286	3533	0.289	3741	0.912	0.937	99.0377	0.284
2.572-2.646	0.289	183	0.246	3380	0.249	3586	0.937	0.956	99.3586	0.243
2.646-2.728	0.272	174	0.234	3325	0.236	3522	0.957	0.963	99.347	0.232
2.728-2.817	0.254	174	0.214	3205	0.216	3421	0.96	0.969	98.7723	0.212
2.817-2.916	0.274	165	0.209	3108	0.212	3295	0.951	0.972	99.3323	0.206
2.916-3.026	0.247	163	0.2	3001	0.202	3210	0.958	0.974	98.567	0.198
3.026-3.149	0.23	166	0.187	2822	0.189	3046	0.966	0.979	98.0959	0.187
3.149-3.289	0.253	123	0.191	2790	0.194	2977	0.957	0.977	97.8502	0.195
3.289-3.449	0.23	133	0.183	2565	0.186	2769	0.968	0.98	97.4359	0.189
3.449-3.636	0.238	128	0.183	2489	0.186	2709	0.964	0.979	96.6039	0.194
3.636-3.856	0.213	112	0.176	2319	0.177	2517	0.969	0.981	96.5832	0.192
3.856-4.121	0.216	102	0.177	2201	0.179	2380	0.972	0.98	96.7647	0.2
4.121-4.451	0.18	114	0.148	2057	0.15	2229	0.981	0.986	97.3979	0.174
4.451-4.874	0.204	84	0.154	1887	0.156	2038	0.977	0.986	96.7125	0.185
4.874-5.448	0.185	100	0.168	1699	0.169	1848	0.979	0.985	97.3485	0.199
5.448-6.287	0.227	73	0.186	1521	0.188	1653	0.976	0.982	96.4307	0.219
6.287-7.69	0.2	67	0.181	1253	0.182	1378	0.978	0.981	95.791	0.218
7.69-10.834	0.156	32	0.147	1015	0.147	1083	0.988	0.988	96.6759	0.178
10.834-88.725	0.153	43	0.182	551	0.18	621	0.989	0.98	95.6522	0.219

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	0.5478	-0.4453	0.1367	0.8917	0.0823	0.2863	0.096	0.2559	0.1151	0.0918	-0.0416	0.0062	0.05	0.0443	-0.0544	0.185	0.0615	0.0816	0.2345	0.1353	0.1214	2.4559	0.057	4.1267
2	0.6591	-0.2937	-0.3067	0.6802	0.0617	0.192	-0.0295	0.2549	-0.1223	0.0885	-0.0132	-0.0351	-0.0225	-0.0778	0.0427	0.1839	-0.0034	0.0121	0.1989	-0.1003	0.0552	23.0723	-36.6725	2.8569
3	1.0579	-0.0061	-0.3649	0.2657	0.0107	0.1703	0.1649	-0.2534	0.2499	-0.0643	-0.0377	0.0826	-0.0323	0.0713	-0.1272	0.2882	-0.0329	0.0772	0.1171	-0.0682	0.1394	7.0571	-0.2141	49.7722
4	0.8109	-0.4675	-0.2416	0.9531	-0.2796	0.3684	-0.0486	-0.1812	-0.2544	-0.0125	0.0043	0.1006	-0.025	0.0696	0.0443	0.2608	-0.0107	0.032	0.111	0.1179	0.1403	18.3806	-40.2662	48.5598

Refinement TLS group

Selection: ALL

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi