PDB-4rhx: Structures of Mycobacterium tuberculosis 6-oxopurine phosphoribos...

ID or keywords:

Entry

Database: PDB / ID: 4rhx

Title

Structures of Mycobacterium tuberculosis 6-oxopurine phosphoribosyltransferase which is a potential target for drug development against this disease

Components

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

transferase/transferase inhibitor / 6-oxopurine phosphoribosyltransferase / Cytoplasmic / transferase-transferase inhibitor complex

Function / homology

Function and homology information

IMP biosynthetic process / purine-containing compound salvage / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / GMP biosynthetic process ...
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.0322 Å

Authors

Eng, W.S. / Hockova, D. / Spacek, P. / West, N.P. / Woods, K. / Naesens, L.M.J. / Keough, D.T. / Guddat, L.W.

Citation

Journal: J.Med.Chem. / Year: 2015
Title: First Crystal Structures of Mycobacterium tuberculosis 6-Oxopurine Phosphoribosyltransferase: Complexes with GMP and Pyrophosphate and with Acyclic Nucleoside Phosphonates Whose Prodrugs Have ...
Authors: Eng, W.S. / Hockova, D. / Spacek, P. / Janeba, Z. / West, N.P. / Woods, K. / Naesens, L.M. / Keough, D.T. / Guddat, L.W.

History

Deposition	Oct 3, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 20, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4rhx.cif.gz	312.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4rhx.ent.gz	257.8 KB	Display	PDB format
PDBx/mmJSON format	4rhx.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4rhx_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	4rhx_full_validation.pdf.gz	3 MB	Display
Data in XML	4rhx_validation.xml.gz	36 KB	Display
Data in CIF	4rhx_validation.cif.gz	49.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rh/4rhx ftp://data.pdbj.org/pub/pdb/validation_reports/rh/4rhx	HTTPS FTP

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Related structure data

Related structure data	4rhtC 4rhuC 4rhyC C: citing same article (ref.)
Similar structure data	1odz-d 4fvk-d 6gs2-1 2c29-d 1t5c-d 4bzf-d 2gft-d 5tt5-d 4qne-d 2nnl-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 (6)

Deposited unit

A: Hypoxanthine-guanine phosphoribosyltransferase

B: Hypoxanthine-guanine phosphoribosyltransferase

C: Hypoxanthine-guanine phosphoribosyltransferase

D: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

A: Hypoxanthine-guanine phosphoribosyltransferase

B: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

3

C: Hypoxanthine-guanine phosphoribosyltransferase

D: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.439, 85.723, 88.139
Angle α, β, γ (deg.)	90.00, 98.77, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Hypoxanthine-guanine phosphoribosyltransferase Mass: 22140.918 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: This sequence occurs naturally in Mycobacterium tuberculosis Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: A5U8U8, UniProt: P9WHQ9*PLUS
#2: Chemical	ChemComp-3QF / [2-([2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl]{2-[(2-oxoethyl)(2-phosphonoethyl)amino]ethyl}amino)ethyl]phosphonic acid Mass: 495.365 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₇N₇O₈P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.25 Å³/Da / Density % sol: 45.4 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG8000, 0.1M Tris-HCl pH8.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 25, 2014
Radiation	Monochromator: None / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95369 Å / Relative weight: 1
Reflection	Resolution: 2.03→48.56 Å / Num. all: 50489 / Num. obs: 50489 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASES		phasing
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.0322→44.966 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.83 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2261	1999	3.96 %	Random
R_work	0.1867	-	-	-
all	0.1887	50461	-	-
obs	0.1882	50461	99.56 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.0322→44.966 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5568	0	136	552	6256

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5999
X-RAY DIFFRACTION	f_angle_d	0.657	8110
X-RAY DIFFRACTION	f_dihedral_angle_d	14.14	2306
X-RAY DIFFRACTION	f_chiral_restr	0.024	919
X-RAY DIFFRACTION	f_plane_restr	0.003	1005

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 (%)
2.0322-2.083	0.2937	136	0.2632	3278	X-RAY DIFFRACTION	94
2.083-2.1394	0.2876	144	0.2415	3494	X-RAY DIFFRACTION	100
2.1394-2.2023	0.2817	140	0.2474	3426	X-RAY DIFFRACTION	100
2.2023-2.2734	0.3959	142	0.3168	3437	X-RAY DIFFRACTION	100
2.2734-2.3546	0.2886	143	0.2354	3466	X-RAY DIFFRACTION	100
2.3546-2.4489	0.2594	144	0.2076	3494	X-RAY DIFFRACTION	100
2.4489-2.5604	0.243	143	0.1939	3453	X-RAY DIFFRACTION	100
2.5604-2.6953	0.2243	142	0.1965	3438	X-RAY DIFFRACTION	100
2.6953-2.8642	0.2196	143	0.1975	3493	X-RAY DIFFRACTION	100
2.8642-3.0853	0.229	144	0.1901	3467	X-RAY DIFFRACTION	100
3.0853-3.3957	0.2253	143	0.1786	3480	X-RAY DIFFRACTION	100
3.3957-3.8868	0.188	144	0.1575	3483	X-RAY DIFFRACTION	100
3.8868-4.896	0.177	145	0.134	3519	X-RAY DIFFRACTION	100
4.896-44.9766	0.1802	146	0.1525	3534	X-RAY DIFFRACTION	100

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	4.6556	-5.1168	-0.6369	7.9146	-1.0235	1.4646	-0.1347	-0.6789	0.154	1.1204	0.4426	-1.2581	0.1472	0.7086	-0.0948	0.6046	0.0731	-0.2117	0.378	-0.0149	0.2546	-5.1563	7.3562	141.8628
2	9.2717	-1.5142	5.864	3.8935	-1.9575	4.9891	0.0157	-0.0519	0.2317	0.5765	-0.2698	0.4764	0.2443	-0.3369	0.006	0.2716	0.0042	0.0966	0.1039	0.0004	0.2339	-24.8796	9.928	130.4089
3	5.0442	0.1245	2.1659	2.4026	0.3996	4.3865	0.0902	0.0631	-0.0274	0.0025	-0.0603	0.1307	0.2689	-0.2108	-0.0282	0.1669	-0.0057	-0.0002	0.0951	0.0178	0.1809	-22.1704	3.8411	118.7766
4	3.4139	1.7623	-5.2966	2.0275	-1.7124	9.1222	0.2739	-0.3219	-0.2074	0.1212	-0.1325	-0.6164	-0.8003	0.9383	-0.1887	0.2165	0.01	0.0061	0.2958	0.0505	0.2914	1.7922	12.2366	114.8345
5	4.5201	0.5622	0.1244	0.8611	-0.0842	2.0396	-0.0035	0.2769	-0.1703	-0.1145	-0.0254	-0.0103	0.0789	0.0488	0.0144	0.1608	0.0243	0.0143	0.1519	0.0289	0.1805	-11.8331	9.8516	112.188
6	1.4601	0.7221	2.3233	3.8589	2.49	5.5802	-0.176	0.1281	0.2173	-0.1819	0.1454	0.0514	-0.4498	-0.0722	0.0413	0.1366	0.0179	0.0224	0.1335	0.0411	0.1747	-16.0202	17.4243	119.3486
7	9.453	6.5685	-5.8361	8.4677	-4.3717	3.8144	0.0117	0.4915	0.5772	-0.3002	0.2238	0.3453	-0.2742	-0.3181	-0.1335	0.169	0.0386	0.0102	0.0941	0.0374	0.1973	-17.9091	19.0897	121.8293
8	8.7415	-1.8141	-0.5824	6.9779	1.2633	4.2207	-0.0706	-0.1165	-0.0419	0.4634	0.135	-0.4679	-0.1373	0.434	-0.0801	0.2	-0.0097	-0.0393	0.1602	0.0155	0.0896	-4.4937	9.6108	132.0771
9	4.6913	-0.0605	2.2593	7.408	1.8989	7.6275	-0.2968	-0.4897	0.0669	0.8019	0.8996	-1.5626	-0.654	1.3021	-0.405	0.4375	-0.0085	-0.0723	0.417	-0.1508	0.4384	-1.7934	9.9545	138.657
10	4.5248	0.9342	0.5136	1.8445	0.2323	2.6007	0.0434	-0.3455	0.0644	0.2854	-0.0926	-0.113	0.1407	0.0469	0.0666	0.2363	0.0219	-0.017	0.1046	-0.0148	0.1612	-13.226	-8.7994	130.2598
11	8.2103	0.2923	7.4988	4.2698	-1.8826	7.9599	-0.6817	1.2696	0.2943	-0.486	0.5357	-0.0827	-0.706	0.9969	0.1863	0.3332	-0.0732	0.0138	0.5897	0.0004	0.4022	-0.4817	-7.7887	116.3114
12	6.6416	2.7086	0.4263	3.5334	0.9212	2.1767	-0.1687	0.1808	-0.3297	-0.0726	0.2436	-0.5527	0.299	0.446	-0.0872	0.2428	0.0723	-0.0153	0.1802	-0.0155	0.2606	-3.3525	-16.23	121.4821
13	3.1052	-0.2505	1.172	3.2482	-0.8018	4.1054	-0.0672	0.1025	-0.159	-0.1341	0.0232	-0.0794	0.3379	-0.172	0.0341	0.1755	-0.0408	0.033	0.11	-0.0219	0.133	-21.7176	-16.2335	119.9811
14	5.7781	0.0843	2.4303	3.3412	-0.1148	4.6764	0.4806	-0.2014	-0.4613	-0.1232	-0.1519	-0.1801	0.6601	0.5105	-0.365	0.2185	0.0671	0.0355	0.3259	0.0275	0.1696	15.6173	14.0647	80.9189
15	4.3358	-0.8413	1.8037	2.8728	-0.1163	2.7468	0.0062	-0.1211	0.1858	0.0844	-0.1674	-0.2379	-0.2443	0.7979	0.1361	0.1647	-0.0547	0.029	0.4633	0.059	0.2197	17.6134	23.418	88.6934
16	8.7024	-0.2262	1.2206	1.8431	1.6585	1.6779	-0.2251	-0.4526	0.9164	0.0797	-0.2889	-0.1624	-1.5891	0.6896	0.4929	0.7488	-0.326	-0.0935	0.5083	0.0499	0.4483	18.8369	36.9349	85.8801
17	4.6092	1.4178	1.6473	3.0933	0.2295	0.8351	0.1534	0.2199	0.306	-0.1107	-0.2437	-0.1528	-0.4987	1.4082	0.0943	0.3305	-0.1932	0.0635	0.7361	0.0858	0.2673	22.7798	29.2858	78.471
18	1.0952	-0.2134	0.7456	2.5688	0.2841	0.6126	0.4476	0.9189	0.8493	-0.8252	-0.0018	-1.2993	-0.3867	1.8424	-0.3837	0.494	0.0056	0.2977	1.179	0.0416	0.4708	24.323	23.2578	71.049
19	6.8896	-1.7243	2.9454	3.8286	-0.7318	6.1552	0.299	0.1191	-0.2252	-0.4002	0.0024	0.2029	0.4512	-0.0272	-0.3018	0.2133	-0.0032	-0.0643	0.173	0.0296	0.1737	3.4624	20.9354	71.3146
20	5.7298	-2.2635	2.674	3.9697	-1.5241	5.1089	0.2891	0.2473	-0.2976	-0.1532	0.006	0.357	0.4646	-0.1766	-0.3023	0.1639	-0.0113	0.0429	0.2418	0.0465	0.1666	0.7401	14.486	95.6223
21	3.0863	1.9874	1.5886	4.16	1.7418	4.65	0.0656	0.1745	0.0653	-0.2381	-0.0327	-0.0505	-0.2662	-0.191	-0.0276	0.1403	0.031	0.0388	0.2961	0.0554	0.1707	0.7478	24.0742	88.0394
22	7.9103	1.9236	5.2452	4.8922	-1.1251	8.2689	-0.5262	0.6523	0.8697	-0.4932	0.237	-0.1683	-1.5347	0.4392	0.3068	0.6469	-0.0146	0.1591	0.2833	0.0814	0.4285	1.4057	37.6243	90.415
23	1.782	-0.2561	-1.2147	1.8836	-0.334	3.7734	0.2271	-0.0002	0.2031	0.082	-0.1197	0.0488	-0.5619	0.0587	-0.0854	0.1962	-0.0194	0.0163	0.2095	0.0284	0.2111	0.1671	27.2371	101.6358
24	4.8487	-1.0696	-0.2809	8.0085	-1.0168	2.107	-0.0519	-0.4047	0.271	0.9962	0.1457	-0.3455	0.372	0.971	0.0911	0.183	0.0126	-0.0218	0.5329	0.0631	0.2619	16.9908	18.9599	105.5206

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 17 through 29 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 47 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 88 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 89 through 102 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 103 through 141 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 142 through 159 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 160 through 169 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 170 through 189 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 190 through 201 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 16 through 88 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 89 through 116 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 117 through 151 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 152 through 202 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 16 through 55 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 56 through 88 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 89 through 116 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 117 through 154 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 155 through 168 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 169 through 202 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 18 through 55 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 56 through 88 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 89 through 116 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 117 through 186 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 187 through 201 )

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Yorodumi