PDB-5knq: Crystal structure of Mycobacterium tuberculosis hypoxanthine guan...

ID or keywords:

Entry

Database: PDB / ID: 5knq

Title

Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with [3S,4R]-(4-(Guanin-9-yl)pyrrolidin-3-yl)oxymethanephosphonic acid and pyrophosphate

Components

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

TRANSFERASE/INHIBITOR / Phosphoribosyltransferase / Inhibitor / Complex / pyrrolidne nucleoside phosphonate / TRANSFERASE-INHIBITOR complex

Function / homology

Function and homology information

IMP biosynthetic process / purine-containing compound salvage / hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / guanine salvage / hypoxanthine metabolic process / 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: 2.553 Å

Authors

Eng, W.S. / Rejman, D. / Keough, D.T. / Guddat, L.W.

Citation

Journal: To Be Published
Title: Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with pyrrolidine nucleoside phosphonate
Authors: Eng, W.S. / Rejman, D. / Keough, D.T. / Guddat, L.W.

History

Deposition	Jun 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn 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_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.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.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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5knq.cif.gz	301.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5knq.ent.gz	246.1 KB	Display	PDB format
PDBx/mmJSON format	5knq.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/kn/5knq ftp://data.pdbj.org/pub/pdb/validation_reports/kn/5knq	HTTPS FTP

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Related structure data

Related structure data	5knpC 5knyC 4rhtS 5knr 5kns 5knt 5knu 5knv 5knx C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4lyy-d 5kny-d 1p19-3 5knv-1 5kns-1 4rhu-1 5knt-1 3kb8-d 4rhy-d 1yfz-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 (7) #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

B: Hypoxanthine-guanine phosphoribosyltransferase

C: Hypoxanthine-guanine phosphoribosyltransferase

D: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

94.1 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
47 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
47 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	56.262, 85.507, 81.468
Angle α, β, γ (deg.)	90.000, 107.220, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Hypoxanthine-guanine phosphoribosyltransferase / HGPRTase Mass: 22969.801 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: hpt, hprT, Rv3624c, MTCY15C10.28 / Production host: Escherichia coli (E. coli) References: UniProt: P9WHQ9, hypoxanthine phosphoribosyltransferase
#2: Chemical	ChemComp-6W8 / [(3~{S},4~{R})-4-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)pyrrolidin-3-yl]oxymethylphosphonic acid / [3S,4R]-(4-(Guanin-9-yl)pyrrolidin-3-yl)oxymethanephosphonic acid Mass: 330.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₆O₅P
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-POP / PYROPHOSPHATE 2- Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H₂O₇P₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.04 Å³/Da / Density % sol: 39.62 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% PEG8000, 0.1 M Tris-HCl pH 8.5 and 0.2 M MgCl2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 20, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.55→45.5 Å / Num. obs: 23974 / % possible obs: 99.6 % / Redundancy: 3.8 % / R_merge(I) obs: 0.084 / Net I/σ(I): 10.6
Reflection shell	Resolution: 2.55→2.67 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.697 / Mean I/σ(I) obs: 1.5 / % possible all: 99

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4RHT

4rht

Resolution: 2.553→42.754 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.96

	R_factor	Num. reflection	% reflection
R_free	0.2367	1988	8.3 %
R_work	0.187	-	-
obs	0.1911	23947	99.57 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 228.34 Å² / B_iso mean: 69.1352 Å² / B_iso min: 20.49 Å²

Refinement step

Cycle: final / Resolution: 2.553→42.754 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5442	0	132	140	5714
B_iso mean	-	-	97.85	54.72	-
Num. residues	-	-	-	-	726

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5708
X-RAY DIFFRACTION	f_angle_d	0.757	7763
X-RAY DIFFRACTION	f_chiral_restr	0.028	933
X-RAY DIFFRACTION	f_plane_restr	0.003	978
X-RAY DIFFRACTION	f_dihedral_angle_d	13.836	1973

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.5532-2.6171	0.3288	136	0.2663	1530	1666	98
2.6171-2.6878	0.3732	137	0.2759	1568	1705	100
2.6878-2.7669	0.3582	146	0.282	1538	1684	100
2.7669-2.8562	0.3217	142	0.2653	1560	1702	100
2.8562-2.9583	0.2715	136	0.2302	1579	1715	100
2.9583-3.0767	0.2501	152	0.2217	1557	1709	100
3.0767-3.2167	0.2943	147	0.2138	1560	1707	100
3.2167-3.3862	0.2639	139	0.192	1577	1716	100
3.3862-3.5982	0.2202	146	0.1839	1562	1708	100
3.5982-3.8759	0.2631	144	0.1765	1579	1723	100
3.8759-4.2656	0.1917	141	0.1583	1569	1710	99
4.2656-4.8821	0.179	140	0.1394	1582	1722	100
4.8821-6.148	0.1889	139	0.1741	1594	1733	100
6.148-42.7595	0.2226	143	0.1669	1604	1747	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	9.078	-0.2763	0.066	3.9315	0.1842	2.9251	-0.1052	-0.3135	-0.2265	0.7085	-0.0241	0.0027	-0.1438	0.2194	0.1454	0.5362	0.0411	0.0078	0.2894	0.052	0.3106	49.0355	101.0993	117.6604
2	1.0449	0.1374	2.2431	5.7373	0.2088	6.5147	-0.1863	-0.4382	-0.2174	0.383	0.127	0.3732	-0.2585	-0.5854	0.1049	0.2961	0.0479	0.0839	0.3044	0.036	0.3867	36.5168	95.9292	108.0401
3	6.0255	-1.8253	-3.1715	2.1042	0.7819	7.401	0.1897	0.4212	0.3006	-0.427	0.0249	0.272	-0.4158	0.0342	-0.2223	0.3551	-0.0377	-0.0957	0.2686	0.0276	0.4032	41.2432	97.7111	96.0382
4	6.0824	4.3391	0.4185	6.9709	1.1437	6.0032	0.0866	0.4794	0.1605	-0.5017	0.3105	-0.1874	-0.7301	0.1007	-0.3568	0.4548	0.0656	-0.0057	0.3433	-0.0338	0.4437	41.3321	105.3052	98.5142
5	7.6888	1.5641	2.6389	4.3044	2.363	3.2688	-0.2191	0.4412	0.79	-0.1727	0.2559	0.7781	-0.7272	-0.153	-0.0039	0.4818	0.025	-0.0466	0.2698	0.0748	0.4572	40.7391	109.7462	105.4097
6	4.3093	-1.6023	-0.5058	7.3714	1.0842	5.5218	0.0818	0.3994	0.0856	-0.2361	-0.2465	-0.421	-0.4049	0.117	0.1691	0.2302	-0.0074	0.0176	0.3834	-0.0356	0.4441	57.0626	103.3612	108.8391
7	9.4199	-0.7006	1.3634	6.9249	4.5144	4.3411	-0.1944	0.4468	0.3483	-0.2308	0.539	-1.1587	-0.4405	0.1332	-0.4045	0.4694	0.0369	0.022	0.3211	-0.0702	0.5526	62.8981	100.7105	110.8663
8	5.5304	1.6495	-1.7508	4.0976	-0.5908	4.4628	0.1093	-0.26	-0.3434	0.5684	-0.0718	-0.2913	-0.0419	0.1738	0.0295	0.4548	0.0419	-0.0468	0.1876	-0.0297	0.3717	49.3128	80.9693	115.6059
9	1.7803	-0.562	-0.2014	3.5049	-0.0492	5.7963	0.1254	0.0908	-0.3498	-0.4673	0.0087	-0.1561	0.352	-0.0914	-0.1177	0.2642	-0.0338	0.0227	0.2222	-0.0013	0.3629	51.2682	83.6959	100.2592
10	4.1745	0.0204	-3.1101	1.9495	-0.5396	4.4602	-0.0176	0.4064	-0.3332	-0.3676	-0.0828	-0.0103	0.5735	-0.2831	0.0668	0.4338	0.0253	-0.0135	0.2766	-0.0163	0.4737	52.0457	74.0692	101.7719
11	6.8726	-2.1923	0.6325	5.9513	-0.8993	2.716	-0.1037	0.1764	-0.5321	-0.6578	0.2067	0.9233	0.4351	-0.4279	-0.0131	0.4054	-0.0776	0.0111	0.3426	0.0501	0.4473	37.4672	76.7445	109.5411
12	2.8308	0.426	0.3159	0.4743	0.7608	1.4119	-0.1758	1.7197	-0.2183	-0.9602	0.5656	-0.4243	0.6789	0.6612	-0.2069	2.0223	0.1749	0.3436	1.0337	-0.2519	0.2291	56.8933	85.277	57.7655
13	4.8843	-0.18	2.2683	6.9252	1.7878	2.1177	0.1809	0.8932	-0.1787	-1.0353	-0.0502	0.2345	0.8754	0.424	-0.0909	0.9557	0.0201	0.0833	0.5258	-0.0612	0.3935	47.4508	80.8681	68.0139
14	5.4132	1.9125	3.4162	5.8813	1.8177	8.8169	-0.2194	0.3077	-0.4828	-1.3264	0.3938	0.156	0.2911	-0.3368	-0.1162	0.7433	-0.0308	-0.0737	0.4204	0.0097	0.3861	45.9222	81.0434	71.7896
15	2.3654	-0.2401	0.7265	0.5272	-0.9102	2.1324	-0.0608	0.3233	-1.3007	0.2116	-0.1762	-2.8179	0.2669	2.3719	-0.0731	0.7397	-0.0099	0.0657	0.8929	0.0054	1.0571	64.1481	86.288	86.6521
16	3.8808	0.2902	2.3362	3.6655	-1.061	6.7582	-0.132	-0.1145	-0.3155	-0.3024	-0.1181	0.1347	0.9279	-0.7264	0.1709	0.7164	-0.0057	-0.021	0.4199	-0.017	0.4371	45.7308	79.638	82.1421
17	5.3308	-1.1883	2.2231	2.1914	0.2481	6.6509	0.262	-0.0054	-0.0731	-0.7814	-0.5934	-0.1975	1.6798	1.1176	0.1609	1.0205	0.2222	0.0879	0.5398	0.027	0.5295	55.9276	76.8224	76.3437
18	1.7481	2.6108	0.7287	4.7122	-1.0345	5.5273	0.283	0.0088	-0.9841	0.092	0.004	-0.6523	0.1517	2.1937	-0.0672	1.3459	0.4931	0.3367	1.0856	-0.0131	0.6659	64.7607	77.4137	69.2383
19	2.5064	-1.8619	-0.1763	5.8931	2.1467	0.985	-0.2068	0.1872	0.3575	-0.6103	-0.013	-0.9383	0.0781	0.7335	0.1203	0.8059	-0.074	0.2067	0.9597	0.168	0.7261	61.8491	94.4371	64.978
20	3.532	1.3608	0.028	5.6233	0.771	0.8413	-0.0933	0.7474	0.3524	-1.5071	-0.0809	-0.2186	-0.5204	0.3695	0.3038	1.2609	-0.1099	-0.2161	0.7687	0.2335	0.6082	40.3467	100.044	60.0946
21	4.8421	-0.8666	-0.0786	5.4219	1.1966	2.9666	0.1848	0.8422	-0.1079	-0.726	-0.7123	0.1929	-0.8452	0.078	0.3895	0.8876	-0.0125	-0.0844	0.5338	0.0061	0.3806	43.9989	95.7933	67.7132
22	3.5629	1.3889	-0.593	4.3052	-3.5062	4.0191	-0.0575	-0.2476	0.5881	-0.3097	-0.0973	0.3179	-0.5685	0.0772	0.0174	0.6837	-0.0685	-0.067	0.451	-0.0427	0.533	42.4423	98.405	79.3993
23	6.5792	-1.2883	-0.4567	5.4569	-2.4932	7.6918	0.116	0.1122	-0.0615	0.1439	-0.0802	0.854	-0.9244	-0.2905	0.0051	0.6885	0.0247	-0.0983	0.3912	-0.0029	0.6408	36.2509	102.0447	76.7343
24	6.0309	3.9093	3.7848	7.1779	2.1375	4.4117	-0.2922	-0.0896	1.398	-0.0305	-0.3813	1.27	-1.0753	-0.904	0.5762	0.9343	0.1012	-0.2379	0.6163	0.0335	0.7115	32.5762	104.5059	71.0068
25	6.2608	-3.1415	2.8205	5.8943	-2.4993	1.87	0.5072	0.3631	-0.5499	-1.3656	-0.1494	1.1047	0.4382	-0.6609	-0.3197	0.9926	-0.0594	-0.2777	0.7182	-0.0499	0.6319	30.8903	87.1193	65.4065

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 17 through 48 )	A	17 - 48
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 78 )	A	49 - 78
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 79 through 116 )	A	79 - 116
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 117 through 141 )	A	117 - 141
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 142 through 168 )	A	142 - 168
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 169 through 186 )	A	169 - 186
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 187 through 202 )	A	187 - 202
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 17 through 58 )	B	17 - 58
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 59 through 116 )	B	59 - 116
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 117 through 158 )	B	117 - 158
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 159 through 201 )	B	159 - 201
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 20 through 47 )	C	20 - 47
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 48 through 78 )	C	48 - 78
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 79 through 91 )	C	79 - 91
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 92 through 103 )	C	92 - 103
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 104 through 116 )	C	104 - 116
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 117 through 150 )	C	117 - 150
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 151 through 167 )	C	151 - 167
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 168 through 198 )	C	168 - 198
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 21 through 58 )	D	21 - 58
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 59 through 78 )	D	59 - 78
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 79 through 116 )	D	79 - 116
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 117 through 141 )	D	117 - 141
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 142 through 163 )	D	142 - 163
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 164 through 201 )	D	164 - 201

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About Yorodumi

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Yorodumi