PDB-4rht: Crystal structures of Mycobacterium tuberculosis 6-oxopurine phos...

ID or keywords:

Entry

Database: PDB / ID: 4rht

Title

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

Components

Hypoxanthine-guanine phosphoribosyltransferase Hpt

Keywords

TRANSFERASE / 6-oxopurine phosphoribosyltransferases / GMP

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: 2.7633 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_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_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.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	4rht.cif.gz	274.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4rht_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	4rht_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4rht_validation.xml.gz	27.4 KB	Display
Data in CIF	4rht_validation.cif.gz	35.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rh/4rht ftp://data.pdbj.org/pub/pdb/validation_reports/rh/4rht	HTTPS FTP

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Related structure data

Related structure data	4rhuC 4rhxC 4rhyC C: citing same article (ref.)
Similar structure data	2owm-2 5dc5-d 5kny-d 1j7j-3 4rhy-d 5ths-d 4rhu-1 5fcw-d 6zry-d 5knp-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 (8) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1)

Deposited unit

A: Hypoxanthine-guanine phosphoribosyltransferase Hpt

B: Hypoxanthine-guanine phosphoribosyltransferase Hpt

C: Hypoxanthine-guanine phosphoribosyltransferase Hpt

D: Hypoxanthine-guanine phosphoribosyltransferase Hpt

hetero molecules

90.9 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 Hpt

B: Hypoxanthine-guanine phosphoribosyltransferase Hpt

hetero molecules

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

3

C: Hypoxanthine-guanine phosphoribosyltransferase Hpt

D: Hypoxanthine-guanine phosphoribosyltransferase Hpt

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.417, 85.580, 156.644
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Hypoxanthine-guanine phosphoribosyltransferase Hpt 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: I6YCM5, UniProt: P9WHQ9*PLUS
#2: Chemical	ChemComp-POP / PYROPHOSPHATE 2- Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H₂O₇P₂
#3: Chemical	ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₈P
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 44 / 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: 42.39 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG8000, 0.1 M Tris-HCl pH8.5, 0.2 M 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: 2.76→47.103 Å / Num. all: 20023 / Num. obs: 20023 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.76→47.1 Å / % possible all: 100

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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: 2.7633→47.103 Å / SU ML: 0.37 / σ(F): 1.36 / Phase error: 31.81 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2841	1997	10 %	Random
R_work	0.225	-	-	-
all	0.228	19964	-	-
obs	0.2308	19964	99.16 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.7633→47.103 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4967	0	140	44	5151

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5173
X-RAY DIFFRACTION	f_angle_d	0.737	7071
X-RAY DIFFRACTION	f_dihedral_angle_d	13.487	1825
X-RAY DIFFRACTION	f_chiral_restr	0.024	860
X-RAY DIFFRACTION	f_plane_restr	0.003	876

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 (%)
2.7633-2.8324	0.4051	136	0.3491	1216	X-RAY DIFFRACTION	95
2.8324-2.909	0.3548	136	0.2929	1233	X-RAY DIFFRACTION	100
2.909-2.9946	0.3293	142	0.271	1280	X-RAY DIFFRACTION	100
2.9946-3.0912	0.2651	142	0.2509	1272	X-RAY DIFFRACTION	100
3.0912-3.2017	0.315	142	0.2502	1272	X-RAY DIFFRACTION	100
3.2017-3.3298	0.2806	143	0.2456	1294	X-RAY DIFFRACTION	100
3.3298-3.4813	0.2871	139	0.2287	1252	X-RAY DIFFRACTION	100
3.4813-3.6648	0.2777	144	0.2239	1285	X-RAY DIFFRACTION	100
3.6648-3.8943	0.2815	142	0.2227	1285	X-RAY DIFFRACTION	100
3.8943-4.1948	0.2758	144	0.2117	1284	X-RAY DIFFRACTION	100
4.1948-4.6166	0.2566	144	0.1889	1295	X-RAY DIFFRACTION	99
4.6166-5.2839	0.2679	144	0.1884	1310	X-RAY DIFFRACTION	100
5.2839-6.6542	0.2761	148	0.2348	1320	X-RAY DIFFRACTION	99
6.6542-47.1096	0.286	151	0.2221	1369	X-RAY DIFFRACTION	97

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	3.4269	2.2875	-4.9058	6.7424	-2.0136	7.2394	0.1838	-0.7211	-0.0752	0.1061	0.0219	0.2023	0.3629	0.1276	-0.2029	0.4498	-0.051	-0.0907	0.1565	0.022	0.3863	25.9168	74.1395	41.0202
2	7.5074	-2.2215	2.3759	5.249	0.4364	5.4329	0.256	-0.3271	-0.4838	0.0966	0.0333	-0.1514	0.3286	0.3288	-0.0195	0.3593	-0.0053	0.0097	0.3182	-0.0187	0.4741	36.1491	79.4265	27.5425
3	4.3386	-2.0193	2.0955	3.5048	0.1061	5.9294	0.0155	0.4893	-0.1271	-0.9608	-0.0402	-0.0933	0.1688	0.0706	0.0075	0.5187	-0.0878	0.0283	0.2085	-0.0285	0.4906	31.8203	80.434	22.754
4	9.8179	1.9932	-3.0175	8.2871	0.1676	6.6007	0.1752	0.719	-0.2186	-1.3798	0.2149	-0.4698	0.4064	-0.2121	-0.3184	0.5819	0.0094	-0.0061	0.2333	0.0162	0.4479	32.9259	71.0956	22.6372
5	5.8902	0.7381	-1.2921	4.5852	-2.9366	4.9472	0.3751	1.4191	-1.8244	-1.0632	-0.1312	-0.3076	0.9656	-0.6473	-0.2181	0.5806	0.0725	-0.0963	0.2403	-0.0456	0.9406	27.474	63.401	29.2152
6	3.1746	-3.1951	-0.6992	7.9849	-1.7745	4.2446	-0.1152	-0.2739	-0.1682	-0.789	0.1724	0.3813	0.2566	-0.8495	-0.1598	0.4125	-0.0589	-0.0502	0.4116	0.0784	0.4883	13.9781	74.6808	33.4174
7	4.8448	3.2689	1.3686	6.7017	0.0238	5.9207	0.038	-1.4515	0.6062	0.6499	-0.1991	0.2229	-0.4218	-0.2978	0.1759	0.4895	-0.0154	-0.0213	0.2336	-0.0868	0.3765	26.5992	98.0955	40.6916
8	2.9831	-0.2913	0.3305	5.188	-1.0705	8.2726	0.1102	-0.3236	-0.1153	-0.201	0.2532	0.0789	-0.7147	-0.338	-0.211	0.3231	0.0321	-0.0046	0.2285	-0.045	0.4118	18.5258	91.6356	30.6778
9	3.8158	-0.4665	-0.0634	2.8253	-0.7244	4.9332	-0.2126	-0.2484	-0.4804	-0.7145	0.4626	0.5096	-0.3989	-0.2998	-0.1624	0.378	-0.1883	-0.0713	0.1835	-0.1059	0.5569	17.8171	89.8155	26.5232
10	3.7556	-0.6773	-4.5815	2.6849	-1.7601	8.2141	0.2851	0.4464	-0.496	-0.7194	-0.4247	0.0635	-0.2107	0.2533	0.2151	1.0063	0.0231	-0.1089	0.3998	0.0499	0.557	19.3873	92.8096	14.6374
11	4.0152	2.8984	5.676	7.8307	2.7081	9.0987	0.2329	0.7176	-0.4427	-0.8133	0.4543	-1.2153	-0.5641	0.2348	-0.2826	0.4926	0.0864	-0.0147	0.2667	-0.0179	0.4676	22.7662	100.3412	26.3271
12	7.7845	0.9118	5.9454	5.6806	1.9713	7.5427	-0.5717	0.522	0.3323	-1.2956	0.3147	0.3175	-0.7215	0.1981	0.1398	0.7024	-0.0569	-0.1542	0.2955	0.0253	0.5512	20.1503	103.9673	24.3823
13	3.3864	-2.303	-3.2709	7.6157	3.0895	5.8679	0.168	-0.1048	-0.0085	-0.1589	0.0787	-1.207	-0.3731	0.3069	-0.2645	0.2692	0.0414	-0.0597	0.3007	-0.0646	0.5309	38.5317	97.4037	32.394
14	4.5639	0.0896	-0.8303	2.2305	-1.2236	6.0259	-0.6408	0.7473	-0.0922	-1.3045	0.3106	0.4117	0.6193	0.5269	0.1807	1.7235	-0.0879	0.1063	0.6745	-0.0894	0.6586	29.6681	76.6727	-15.2172
15	3.4816	0.3492	-0.3266	4.6992	4.9795	5.4217	0.3472	0.0699	-0.2982	-1.0128	-0.799	-0.0333	0.342	-0.705	0.2418	1.6694	-0.0963	0.0163	0.3886	-0.0917	0.4172	25.4486	77.025	-5.4706
16	5.1508	1.105	1.145	7.9168	4.8308	6.9621	0.4078	-0.5348	-0.1565	0.0633	-0.6115	0.6592	1.1561	-0.6945	0.4289	1.0176	-0.113	0.0466	0.5066	0.0455	0.4065	27.9311	76.2601	5.3314
17	2.5928	-2.9929	0.7162	3.6042	-1.3303	2.2004	0.0469	0.3615	0.3791	-1.5735	-0.3767	-1.1023	0.8603	0.0429	0.4607	1.2178	-0.0774	0.2399	0.5358	-0.1059	0.6475	36.4318	75.7484	-5.6761
18	9.7806	2.83	-1.3436	9.7293	0.1999	5.4411	0.4475	-0.5143	-0.6248	0.1397	0.0774	-2.1672	1.8826	0.3796	-0.1466	1.317	0.0518	0.084	0.4819	-0.1061	0.7119	34.6342	71.9527	3.4617
19	6.6502	2.8094	-0.3253	3.1669	-1.3893	0.8191	-0.5184	1.5224	-1.1937	-0.6819	-0.3457	-1.0118	1.5319	-0.992	-0.2951	1.6799	-0.1429	0.2108	0.7727	-0.2125	0.9559	31.0808	66.6659	-4.8602
20	3.5927	-2.4724	3.0547	6.306	-5.8589	5.6457	0.4806	0.7404	-1.0464	-1.5252	-0.8822	-2.2197	0.8871	0.3232	0.2129	1.1782	0.1104	0.1211	0.8338	-0.1042	0.9257	45.4972	76.013	-9.2359
21	4.5437	-2.0863	1.9725	4.7242	1.0554	1.9792	-0.635	0.9793	-0.5436	-0.4193	-0.0262	-0.5586	0.9481	1.1011	0.188	1.8399	-0.0733	0.5647	0.7836	-0.155	0.6934	40.9125	79.5344	-13.2122
22	7.0048	-0.4112	2.6399	5.8648	0.4853	5.9506	0.8285	0.7033	0.3644	-0.7681	-0.8088	-0.8512	-0.6118	0.6307	0.5007	1.6788	-0.2428	0.2519	0.6213	0.0624	0.7367	37.6105	93.7953	-12.5953
23	7.0993	-3.0009	-0.2863	3.0578	-2.4389	3.733	0.6274	1.6574	-0.778	-1.7701	-0.876	0.3928	-0.9377	-0.3351	-0.1909	2.0602	0.3497	-0.2963	1.1897	0.0022	0.3721	13.4878	90.6746	-20.4955
24	5.3049	-2.8674	-1.8557	2.4303	-1.5314	7.4784	0.025	0.2635	-0.0777	-0.9645	-0.399	-0.1495	0.2711	0.3324	0.4338	1.2506	-0.072	-0.1437	0.4707	-0.1257	0.6239	21.3586	92.7798	-5.2433
25	1.7955	-1.0546	1.936	4.2965	-0.1816	7.0793	0.152	0.2798	-0.2163	-0.4159	-0.0575	-0.0496	-1.3204	-0.1373	-0.1069	1.2184	-0.0048	-0.027	0.4924	0.0132	0.6574	19.4874	95.8259	-1.2545
26	0.1959	-0.2174	-0.8315	1.1485	1.0573	5.6792	0.3433	0.2626	0.5003	-0.1915	-0.4905	0.409	-1.8095	-0.7336	0.0069	1.8446	0.4708	-0.2463	0.7715	0.0397	0.7231	12.8014	99.4414	-4.193
27	2.356	-1.9807	-1.6348	5.8566	3.9861	2.9037	-0.7584	0.5071	-0.9471	1.3917	-0.1216	0.1167	-0.1941	-1.9586	0.6425	0.9829	-0.2024	0.0234	1.4006	-0.132	0.5012	6.061	83.9506	-12.7256
28	2.6304	-1.3767	-3.1177	5.7677	-3.3718	8.6988	0.9189	-0.2462	-0.9764	1.0422	-1.1642	0.7223	0.8236	-0.3582	0.0335	1.0398	-0.2855	-0.18	0.9441	-0.3189	0.8674	10.5746	76.8033	-11.4141

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 22 through 47 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 48 through 68 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 69 through 116 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 117 through 151 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 152 through 168 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 169 through 199 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 21 through 47 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 48 through 78 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 79 through 91 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 92 through 116 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 117 through 128 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 129 through 168 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 169 through 200 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 24 through 78 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 79 through 92 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 93 through 116 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 117 through 129 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 130 through 141 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 142 through 150 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 151 through 161 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 162 through 181 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 182 through 196 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 22 through 47 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 48 through 105 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 106 through 130 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 131 through 170 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 171 through 180 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 181 through 198 )

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