PDB-6mxd: Crystal structure of Trypanosoma brucei hypoxanthine-guanine-xant...

ID or keywords:

Entry

Database: PDB / ID: 6mxd

Title

Crystal structure of Trypanosoma brucei hypoxanthine-guanine-xanthine phosphoribosyltranferase in complex with IMP

Components

Hypoxanthine-guanine phosphoribosyltransferase, putative

Keywords

TRANSFERASE / 6-oxopurine PRTs / Purine salvage

Function / homology

Function and homology information

xanthine phosphoribosyltransferase activity / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / glycosome / nuclear lumen / phosphate ion binding ...
Similarity search - Function

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.96 Å

Authors

Teran, D. / Guddat, L.

Citation

Journal: Febs J. / Year: 2019
Title: Crystal structures of Trypanosoma brucei hypoxanthine - guanine - xanthine phosphoribosyltransferase in complex with IMP, GMP and XMP.
Authors: Teran, D. / Dolezelova, E. / Keough, D.T. / Hockova, D. / Zikova, A. / Guddat, L.W.

History

Deposition	Oct 30, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 24, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Oct 11, 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	6mxd.cif.gz	356.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6mxd.ent.gz	290.2 KB	Display	PDB format
PDBx/mmJSON format	6mxd.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/mx/6mxd ftp://data.pdbj.org/pub/pdb/validation_reports/mx/6mxd	HTTPS FTP

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Related structure data

Related structure data	6mxbC 6mxcC 6mxgC 1tc2S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5o5k-1 2p6g-5 3v9x-1 4mv6-d 1vlc-d 6mxc-2 2g5f-1 4tpj-1 2e1z-d 1xac-d 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 (3)

Deposited unit

A: Hypoxanthine-guanine phosphoribosyltransferase, putative

B: Hypoxanthine-guanine phosphoribosyltransferase, putative

C: Hypoxanthine-guanine phosphoribosyltransferase, putative

D: Hypoxanthine-guanine phosphoribosyltransferase, putative

hetero molecules

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

1

A: Hypoxanthine-guanine phosphoribosyltransferase, putative

B: Hypoxanthine-guanine phosphoribosyltransferase, putative

hetero molecules

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

2

C: Hypoxanthine-guanine phosphoribosyltransferase, putative

hetero molecules

D: Hypoxanthine-guanine phosphoribosyltransferase, putative

hetero molecules

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

Unit cell

Length a, b, c (Å)	59.285, 64.984, 79.075
Angle α, β, γ (deg.)	85.74, 74.58, 62.87
Int Tables number	1
Space group name H-M	P1

#1: Protein	Hypoxanthine-guanine phosphoribosyltransferase, putative Mass: 30638.998 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote) Strain: 927/4 GUTat10.1 / Gene: Tb10.70.6660 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38CA1
#2: Chemical	ChemComp-IMP / INOSINIC ACID Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₄O₈P
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.13 Å³/Da / Density % sol: 42.24 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 25% PEG 3350, 0.2 M lithium sulphate and 0.1 M Bis-Tris pH 5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 6, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.96→47.268 Å / Num. obs: 20692 / % possible obs: 98.6 % / Redundancy: 2 % / R_merge(I) obs: 0.148 / Net I/σ(I): 3.5
Reflection shell	Resolution: 2.96→3.14 Å / Redundancy: 2 % / R_merge(I) obs: 0.397 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6539 / % possible all: 97.3

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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: 1TC2

1tc2

Resolution: 2.96→47.27 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.302	1998	9.67 %
R_work	0.252	-	-
obs	0.257	20670	98.5 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.96→47.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6870	0	95	25	6990

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7102
X-RAY DIFFRACTION	f_angle_d	0.577	9623
X-RAY DIFFRACTION	f_dihedral_angle_d	6.59	4333
X-RAY DIFFRACTION	f_chiral_restr	0.045	1100
X-RAY DIFFRACTION	f_plane_restr	0.003	1213

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 (%)
2.963-3.0371	0.4275	124	0.3425	1288	X-RAY DIFFRACTION	96
3.0371-3.1192	0.3549	152	0.3107	1345	X-RAY DIFFRACTION	97
3.1192-3.211	0.4015	149	0.3085	1324	X-RAY DIFFRACTION	99
3.211-3.3146	0.3522	134	0.2846	1336	X-RAY DIFFRACTION	98
3.3146-3.433	0.3286	151	0.2591	1332	X-RAY DIFFRACTION	99
3.433-3.5704	0.3402	130	0.2739	1324	X-RAY DIFFRACTION	98
3.5704-3.7329	0.3191	155	0.2503	1319	X-RAY DIFFRACTION	98
3.7329-3.9296	0.2766	143	0.2391	1361	X-RAY DIFFRACTION	99
3.9296-4.1757	0.2394	145	0.2265	1306	X-RAY DIFFRACTION	99
4.1757-4.4978	0.2334	138	0.2068	1361	X-RAY DIFFRACTION	99
4.4978-4.95	0.2945	149	0.212	1350	X-RAY DIFFRACTION	99
4.95-5.6653	0.2788	140	0.236	1332	X-RAY DIFFRACTION	99
5.6653-7.1337	0.2649	150	0.2688	1354	X-RAY DIFFRACTION	99
7.1337-47.2744	0.2587	138	0.2302	1340	X-RAY DIFFRACTION	99

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	0.7913	1.0035	-0.8035	1.7152	-0.2741	1.4895	0.0005	-0.0909	0.075	-0.0634	0.0062	-0.0808	-0.082	0.1323	-0.0151	0.1963	0.0239	0.0157	0.2448	-0.0242	0.344	51.5803	2.7426	-11.1398
2	2.3708	0.3735	-1.8672	5.8679	-1.5579	2.4339	0.0419	-0.3804	-0.3786	0.468	-0.152	-0.468	-0.0869	-0.7146	0.2234	0.2536	-0.0668	-0.0688	0.4035	-0.0132	0.2901	27.7246	-23.131	-22.7229
3	2.0442	-1.2384	0.7449	5.6266	-1.9192	0.9507	-0.2135	0.2912	0.3912	-0.6276	0.2295	-0.3309	0.2289	-0.0938	0.2016	0.2714	0.0084	0.0685	0.5947	-0.0244	0.2905	26.0483	1.2153	-24.3157
4	2.9009	-1.3965	0.3731	0.9867	-1.2279	3.5535	0.5376	0.1649	0.357	-0.1167	-0.5101	-0.253	-0.6149	0.4362	0.181	0.6336	0.04	0.0314	0.1301	-0.0065	0.7274	31.2746	23.0751	-14.5259
5	0.3712	-0.4812	0.0084	1.2531	-1.252	3.2013	0.0905	0.087	0.3342	-0.5137	-0.2185	-0.4167	0.6021	-0.4549	-0.0215	0.1997	0.0172	-0.011	0.2878	-0.0045	0.2527	32.4646	1.6384	-15.4822
6	5.2413	1.5413	-0.1533	0.5164	0.1784	0.3533	0.2709	-1.296	0.1741	-0.0678	-0.234	-0.6487	-0.1104	0.0778	0.0256	0.4035	0.0836	0.0524	0.3876	-0.1169	0.2259	29.5592	5.8937	-6.5393
7	1.6321	-0.3955	-1.0758	2.6562	-0.8397	1.1464	0.0072	-0.1874	0.0989	0.2422	0.2225	0.3025	-0.1016	-0.2917	-0.1692	0.26	0.0768	-0.0112	0.3921	0.004	0.297	19.0439	0.7053	-8.108
8	0.8554	0.407	0.7474	0.7879	0.9681	1.201	-0.2409	-0.4202	0.2341	-0.0162	-0.3477	-0.2369	0.2307	-0.2357	-0.2541	0.361	0.0904	-0.0057	0.0512	0.121	0.5761	29.8289	-18.4007	-9.5833
9	1.3766	-0.5645	-0.0705	1.1165	0.9868	1.3867	0.0599	-0.0627	-0.2122	0.3032	-0.0749	-0.3401	0.1459	-0.1354	0.0589	0.2145	-0.0448	0.0533	0.2636	0.0727	0.2763	58.1124	-12.948	-37.7672
10	1.054	-0.171	1.0197	1.2573	0.0248	1.0181	-0.1395	-0.1089	-0.0413	0.1107	0.0332	-0.4033	-0.0853	-0.4306	-0.0165	0.1811	-0.0665	0.0734	0.3439	-0.0092	0.3885	62.1681	-14.9417	-43.5726
11	1.5869	-0.6111	-0.3775	0.4545	-0.075	0.1007	-0.0167	0.209	-0.0713	-0.2033	-0.1046	0.148	0.0598	0.1206	0.1666	0.4017	-0.07	-0.1298	0.2371	-0.0658	0.4248	59.248	-19.6121	-51.7303
12	1.4186	-0.2283	1.1463	3.453	-0.1586	0.8845	0.0188	0.1186	0.0138	0.2396	-0.0644	0.5155	0.0802	-0.2703	0.0367	0.2695	-0.0598	0.0161	0.4487	-0.0054	0.2805	48.5875	-14.3549	-50.6025
13	1.5939	-0.1254	-0.89	0.9976	0.8025	1.1371	0.1501	0.3226	0.0723	-0.1986	-0.082	-0.1717	-0.2213	0.245	-0.1191	0.2786	-0.0393	-0.0187	0.2532	-0.0214	0.2579	59.5033	4.7253	-49.0865
14	1.4138	-0.7532	0.8772	2.9291	-1.6082	1.4623	0.0742	0.1971	0.1429	0.0473	0.0013	0.0688	-0.1844	0.0326	-0.0768	0.2543	0.0052	0.0742	0.2789	-0.0552	0.202	15.1755	-5.6487	-43.9086
15	0.6728	0.0565	-0.2137	1.7088	-0.2614	0.4096	-0.0515	0.1263	-0.1548	-0.1054	-0.0278	-0.3616	-0.0015	0.2748	0.0806	0.2188	-0.0331	0.0025	0.3855	-0.0055	0.3186	21.5963	-14.4307	-48.6274
16	2.2443	0.7017	0.6076	0.722	0.1855	0.8757	-0.2055	0.5139	0.4438	-0.0762	0.3025	0.2889	-0.3753	0.0086	0.0775	0.0721	0.022	-0.0284	0.2825	0.0284	0.4491	46.8333	8.4161	-31.6425
17	1.3729	-0.4071	0.5247	0.664	0.1232	2.0397	0.1096	-0.0909	-0.1823	0.0712	0.1375	0.1684	0.1563	0.2823	-0.2539	0.3113	0.0505	0.0618	0.2828	0.035	0.2723	44.8513	-15.6284	-11.7172
18	5.1469	1.5874	-1.6543	0.7402	-0.7241	0.9235	0.6196	-0.7089	0.6149	0.2688	-0.1755	0.0353	0.0942	0.7278	-0.0153	0.4694	0.1103	-0.1358	0.2609	0.145	0.0652	45.6312	-7.2735	-3.122

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 154 THROUGH 234 )
2	X-RAY DIFFRACTION	2	CHAIN 'B' AND (RESID 9 THROUGH 36 )
3	X-RAY DIFFRACTION	3	CHAIN 'B' AND (RESID 37 THROUGH 55 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 56 THROUGH 79 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 80 THROUGH 103 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 104 THROUGH 153 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 154 THROUGH 203 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 204 THROUGH 234 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 6 THROUGH 79 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 80 THROUGH 102 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 103 THROUGH 153 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 154 THROUGH 203 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 204 THROUGH 234 )
14	X-RAY DIFFRACTION	14	CHAIN 'D' AND (RESID 7 THROUGH 135 )
15	X-RAY DIFFRACTION	15	CHAIN 'D' AND (RESID 136 THROUGH 234 )
16	X-RAY DIFFRACTION	16	CHAIN 'A' AND (RESID 6 THROUGH 36 )
17	X-RAY DIFFRACTION	17	CHAIN 'A' AND (RESID 37 THROUGH 103 )
18	X-RAY DIFFRACTION	18	CHAIN 'A' AND (RESID 104 THROUGH 153 )

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