PDB-6apt: Trypanosoma brucei hypoxanthine guanine phosphoribosyltransferase...

ID or keywords:

Entry

Database: PDB / ID: 6apt

Title

Trypanosoma brucei hypoxanthine guanine phosphoribosyltransferase in complex with {[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)

Components

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

TRANSFERASE / Trypanosoma brucei / Purine salvage / acyclic nucleoside biphosphonate

Function / homology

Function and homology information

hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / glycosome / ciliary plasm / nuclear lumen ...
Similarity search - Function

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.795 Å

Authors

Teran, D. / Guddat, L.W.

Citation

Journal: PLoS Negl Trop Dis / Year: 2018
Title: Evaluation of the Trypanosoma brucei 6-oxopurine salvage pathway as a potential target for drug discovery.
Authors: Dolezelova, E. / Teran, D. / Gahura, O. / Kotrbova, Z. / Prochazkova, M. / Keough, D. / Spacek, P. / Hockova, D. / Guddat, L. / Zikova, A.

History

Deposition	Aug 17, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6apt.cif.gz	157.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6apt.ent.gz	124 KB	Display	PDB format
PDBx/mmJSON format	6apt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6apt_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6apt_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6apt_validation.xml.gz	18.9 KB	Display
Data in CIF	6apt_validation.cif.gz	26.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ap/6apt ftp://data.pdbj.org/pub/pdb/validation_reports/ap/6apt	HTTPS FTP

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Related structure data

Related structure data	6apsC 6apuC 6apvC 6aqoC 6ar9C 5jsqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5k51-1 5k51-2 6mxg-d 6wq1-1 5kam-2 5jsq-d 2ij5-2 5dy9-1 5kap-2 5kap-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (6)

Deposited unit

A: Hypoxanthine-guanine phosphoribosyltransferase

B: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

1

A: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

A: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

defined by author&software
Evidence: SAXS
49.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

B: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

defined by author&software
49.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	44.676, 94.401, 110.016
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	17
Space group name H-M	P222₁

#1: Protein	Hypoxanthine-guanine phosphoribosyltransferase / HGPRTase Mass: 24221.775 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HGPRT / Production host: Escherichia coli (E. coli) References: UniProt: Q07010, hypoxanthine phosphoribosyltransferase
#2: Chemical	ChemComp-45T / {[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid) Mass: 441.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₂₁N₅O₉P₂
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.63 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 25% PEG 3350, 0.2 M lithium sulfate and 0.1 M Bis-Tris PH range: 5-7

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 6, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95369 Å / Relative weight: 1
Reflection	Resolution: 1.79→47.53 Å / Num. obs: 43878 / % possible obs: 98.8 % / Redundancy: 5.5 % / R_pim(I) all: 0.045 / Net I/σ(I): 11.3
Reflection shell	Resolution: 1.79→1.83 Å / Redundancy: 9.9 % / R_merge(I) obs: 0.929 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2272 / R_pim(I) all: 0.316 / % possible all: 88

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5JSQ

5jsq

Resolution: 1.795→44.676 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.11 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.212	1999	4.56 %
R_work	0.1984	-	-
obs	0.1991	43805	98.74 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.795→44.676 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2668	0	70	267	3005

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	2804
X-RAY DIFFRACTION	f_angle_d	1.244	3814
X-RAY DIFFRACTION	f_dihedral_angle_d	12.772	1990
X-RAY DIFFRACTION	f_chiral_restr	0.075	447
X-RAY DIFFRACTION	f_plane_restr	0.006	472

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7953-1.8402	0.3007	126	0.2723	2636	X-RAY DIFFRACTION	89
1.8402-1.8899	0.2158	142	0.2379	2972	X-RAY DIFFRACTION	100
1.8899-1.9456	0.2889	143	0.2279	2996	X-RAY DIFFRACTION	100
1.9456-2.0084	0.2533	142	0.2169	2962	X-RAY DIFFRACTION	100
2.0084-2.0801	0.2237	143	0.2068	2980	X-RAY DIFFRACTION	100
2.0801-2.1634	0.2155	143	0.1913	3010	X-RAY DIFFRACTION	100
2.1634-2.2619	0.232	143	0.1934	2975	X-RAY DIFFRACTION	100
2.2619-2.3811	0.2325	143	0.1947	3007	X-RAY DIFFRACTION	100
2.3811-2.5303	0.2317	145	0.1926	3001	X-RAY DIFFRACTION	100
2.5303-2.7256	0.2444	143	0.1934	3007	X-RAY DIFFRACTION	100
2.7256-2.9999	0.2017	145	0.1968	3041	X-RAY DIFFRACTION	100
2.9999-3.4338	0.1845	146	0.1881	3059	X-RAY DIFFRACTION	100
3.4338-4.3257	0.1704	147	0.1782	3081	X-RAY DIFFRACTION	100
4.3257-44.6898	0.2135	148	0.2063	3079	X-RAY DIFFRACTION	95

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	0.0184	0.0982	0.0365	0.5661	0.203	0.0731	-0.0503	-0.0084	-0.1227	-0.5944	0.0583	0.2567	-0.2686	0.0033	-0.0545	0.2592	-0.0457	0.0137	0.2091	0.0235	0.1906	3.1176	47.124	-11.5172
2	0.5926	-0.3401	0.0344	0.2249	-0.0464	0.0572	-0.1362	-0.0564	-0.1493	-0.3292	0.189	0.3045	-0.0947	-0.0803	-0.0407	0.211	-0.0378	-0.0757	0.1518	0.0132	0.2184	-1.4681	37.533	-10.5355
3	0.1978	-0.1073	-0.2412	0.0591	0.1327	0.3016	-0.1636	0.073	-0.0228	-0.1467	-0.0782	0.1667	0.0883	-0.1583	-0.1123	0.1419	-0.1436	-0.1895	0.1425	-0.005	0.4659	-8.414	33.8562	-11.782
4	0.5368	-0.1254	-0.3657	0.068	0.1822	0.5109	-0.0742	0.1428	-0.1564	-0.4136	0.1837	0.1883	0.0961	0.1343	-0.0676	0.2236	-0.0562	-0.0801	0.1421	0.0047	0.2023	1.6757	32.9432	-11.1602
5	0.0976	0.0612	0.0179	0.1076	-0.017	0.0329	0.1311	0.0996	-0.1472	-0.2347	0.0004	0.0487	0.0565	0.007	0.0027	0.2452	-0.0514	-0.005	0.1626	-0.0087	0.2677	1.2802	26.9894	-10.1192
6	0.4887	0.1919	0.0093	0.0953	0.0019	0.0576	-0.1564	0.014	0.0051	0.4398	0.2241	-0.2121	0.162	0.0725	0.0243	0.2668	0.0664	-0.0112	0.1403	-0.0162	0.1945	7.3731	33.498	7.2081
7	0.0506	0.0958	-0.0155	0.1787	-0.0277	0.0045	0.0943	-0.0747	-0.1308	-0.0358	-0.0821	-0.1586	0.0649	-0.0101	0.0272	0.8281	-0.1505	-0.0879	0.2387	0.1753	0.245	1.8953	28.3286	19.4217
8	0.0142	-0.0366	0.037	0.2012	-0.0945	0.1007	-0.0086	-0.07	0.0329	0.3729	0.2037	0.0732	-0.1138	-0.0883	0.1865	0.3488	0.4037	0.1239	0.0307	0.0718	0.2423	10.6037	15.2746	10.8994
9	0.3252	-0.0436	-0.1492	1.1121	-0.1732	0.257	0.0282	-0.1115	0.0463	-0.447	0.1494	0.0906	0.047	-0.0988	0.0756	0.1831	-0.021	-0.0288	0.2018	0.0273	0.1174	17.2618	4.7664	-14.2274
10	0.0751	-0.0325	-0.0297	0.2129	-0.1425	0.1084	-0.0257	-0.0982	-0.0048	-0.0716	0.17	0.008	0.028	-0.1076	0.1139	0.0835	-0.026	-0.0327	0.1325	0.0129	0.0717	20.2344	1.6473	-7.4368
11	0.4738	-0.3865	0.1598	0.3489	-0.1773	0.1617	-0.1629	0.0986	0.0901	-0.109	0.0742	-0.3586	-0.0127	0.0347	-0.1409	0.1467	-0.0575	0.1035	0.1535	-0.0317	0.1822	28.3724	9.0406	-10.7405
12	0.194	0.0972	-0.2012	0.0464	-0.1013	0.2271	-0.1344	0.0969	-0.1984	-0.1255	-0.0428	-0.2746	0.0359	0.2061	-0.3207	-0.0992	-0.3121	0.1929	0.038	0.0126	0.3622	35.0986	13.1802	-11.4903
13	0.3976	-0.0484	0.1034	0.1745	-0.2234	0.2845	-0.0987	0.1741	0.1458	-0.3873	0.2072	-0.2837	-0.0506	-0.0239	-0.0734	0.1483	-0.0448	0.0871	0.1256	-0.0042	0.1422	24.7657	14.343	-11.0335
14	0.0153	0.0929	-0.0326	0.4974	-0.1789	0.0642	-0.0065	0.0167	0.2675	-0.2597	0.0132	-0.111	0.0973	0.0863	-0.008	0.1339	-0.0646	0.0113	0.1879	-0.0078	0.2001	25.1253	20.2507	-10.0575
15	0.2956	0.0849	-0.1142	0.0966	-0.0664	0.0633	-0.0764	-0.0669	0.2144	0.3096	0.0789	-0.0592	-0.2787	-0.026	0.0367	0.1952	0.0431	-0.0364	0.1327	-0.0121	0.1242	20.5766	14.8175	6.1777
16	0.2322	0.1102	0.0868	0.0594	0.0661	0.1648	-0.1363	-0.0097	0.0226	0.285	0.2004	0.1236	-0.2683	-0.1153	0.0101	0.2022	0.0812	0.0095	0.17	0.0234	0.1368	15.8394	11.5883	9.3658
17	0.1297	-0.0542	-0.0685	0.0481	0.0147	0.0452	0.0719	-0.0835	0.1273	0.0281	0.0002	-0.0095	-0.1325	0.0443	0.0313	0.7034	0.1108	-0.1496	0.3031	-0.1753	0.3425	23.1834	18.2195	19.697
18	0.0366	0.0245	-0.0439	0.061	-0.0465	0.0572	0.0612	0.1648	-0.1694	0.4989	0.2031	-0.1701	0.0829	0.177	0.0145	0.3564	0.1306	-0.1518	0.2298	-0.0873	0.3396	15.4488	32.0012	10.8629
19	0.0183	0.0912	0.0122	0.7459	0.0745	0.0089	0.0276	0.0131	-0.0061	-0.4515	0.1675	-0.559	-0.0527	0.2555	0.0812	0.2107	-0.0115	0.0848	0.2599	-0.0819	0.27	15.4663	37.9873	-10.0518
20	0.7058	-0.4499	0.0606	1.193	0.2963	0.2783	0.0791	-0.042	0.0703	-0.6664	0.0953	0.0966	-0.0697	0.1322	0.1342	0.2727	-0.0429	0.0092	0.123	-0.0081	0.1594	5.5086	45.5688	-12.0023

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 70 through 79 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 80 through 119 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 120 through 132 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 133 through 148 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 149 through 158 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 159 through 188 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 189 through 197 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 5 through 16 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 17 through 53 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 54 through 79 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 80 through 119 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 120 through 132 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 133 through 148 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 149 through 158 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 159 through 178 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 179 through 188 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 189 through 195 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 5 through 16 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 17 through 34 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 35 through 69 )

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