PDB-7nnv: Crystal structure of Mycobacterium tuberculosis ArgF in complex w...

ID or keywords:

Entry

Database: PDB / ID: 7nnv

Title

Crystal structure of Mycobacterium tuberculosis ArgF in complex with carbamoyl phosphate.

Components

Ornithine carbamoyltransferase

Keywords

TRANSFERASE / ArgF / Ornithine Carbamoyltransferase

Function / homology

Function and homology information

ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / L-arginine biosynthetic process via ornithine / L-arginine biosynthetic process / amino acid binding / cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.67 Å

Authors

Mendes, V. / Gupta, P. / Burgess, A. / Sebastian-Perez, V. / Cattermole, E. / Meghir, C. / Blundell, T.L.

Funding support

United States, 1items

Citation

Journal: Comput Struct Biotechnol J / Year: 2021
Title: A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis
Authors: Gupta, P. / Thomas, S.E. / Zaidan, S.A. / Pasillas, M.A. / Cory-Wright, J. / Sebastian-Perez, V. / Burgess, A. / Cattermole, E. / Meghir, C. / Abell, C. / Coyne, A.G. / Jacobs, W.R. / ...

History

Deposition	Feb 25, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 30, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	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	7nnv.cif.gz	719 KB	Display	PDBx/mmCIF format
PDB format	pdb7nnv.ent.gz	594.6 KB	Display	PDB format
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Validation report

Summary document	7nnv_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	7nnv_full_validation.pdf.gz	2 MB	Display
Data in XML	7nnv_validation.xml.gz	79.7 KB	Display
Data in CIF	7nnv_validation.cif.gz	120.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nn/7nnv ftp://data.pdbj.org/pub/pdb/validation_reports/nn/7nnv	HTTPS FTP

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Related structure data

Related structure data	7nlfC 7nlnC 7nloC 7nlpC 7nlqC 7nlrC 7nlsC 7nltC 7nluC 7nlwC 7nlxC 7nlyC 7nlzC 7nm0C 7nn1C 7nn4C 7nn7C 7nn8C 7nnbC 7nncC 7nnfC 7nniC 7nnqC 7nnrC 7nnwC 7nnyC 7nnzC 7norC 7nosC 7notC 7nouC 7novC 7np0C 7nphC 7npjC 2p2gS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7nnz-1 7nor-1 7nnf-2 7nnw-1 7nos-2 7nov-1 7nnf-1 7nny-1 2i6u-d 2p2g-2 7np0-1 2p2g-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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (7)

Deposited unit

A: Ornithine carbamoyltransferase

B: Ornithine carbamoyltransferase

C: Ornithine carbamoyltransferase

D: Ornithine carbamoyltransferase

E: Ornithine carbamoyltransferase

F: Ornithine carbamoyltransferase

hetero molecules

201 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ornithine carbamoyltransferase

B: Ornithine carbamoyltransferase

C: Ornithine carbamoyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
101 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Ornithine carbamoyltransferase

E: Ornithine carbamoyltransferase

F: Ornithine carbamoyltransferase

hetero molecules

defined by author&software
101 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	91.441, 142.371, 99.023
Angle α, β, γ (deg.)	90.000, 117.170, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Ornithine carbamoyltransferase / OTCase Mass: 33208.324 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: argF, Rv1656, MTCY06H11.21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIT9, ornithine carbamoyltransferase
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-CP / PHOSPHORIC ACID MONO(FORMAMIDE)ESTER Mass: 141.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH₄NO₅P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1803 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.88 Å³/Da / Density % sol: 57.26 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion Details: 150 mM ammonium dihydrogen phosphate 10 mM praseodymium acetate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9795 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 6, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 1.67→88.1 Å / Num. obs: 259225 / % possible obs: 99.2 % / Redundancy: 5.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.056 / R_pim(I) all: 0.026 / R_rim(I) all: 0.062 / Net I/σ(I): 13.6 / Num. measured all: 1330397 / Scaling rejects: 6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.67-1.76	4.2	1.186	151816	36285	0.46	0.634	1.351	0.9	95.2
5.27-88.1	5.2	0.025	43412	8389	0.999	0.012	0.027	47.1	99.8

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	8.05 Å	88.1 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2	refinement
Aimless	0.7.1	data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	3.27	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2P2G

2p2g

Resolution: 1.67→49.55 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1805	13172	5.08 %
R_work	0.1612	245949	-
obs	0.1622	259121	99.2 %

Solvent computation

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

Displacement parameters

B_iso max: 96.07 Å² / B_iso mean: 35.4878 Å² / B_iso min: 19.44 Å²

Refinement step

Cycle: final / Resolution: 1.67→49.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13657	0	117	1806	15580
B_iso mean	-	-	43.19	45.24	-
Num. residues	-	-	-	-	1814

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.67-1.69	0.3458	364	0.3438	7261	7625	88
1.69-1.71	0.3413	380	0.3256	7638	8018	92
1.71-1.73	0.3333	455	0.3078	8110	8565	99
1.73-1.75	0.3029	429	0.2829	8228	8657	100
1.75-1.77	0.2948	452	0.2696	8253	8705	100
1.77-1.8	0.2898	456	0.2469	8235	8691	100
1.8-1.82	0.2762	465	0.2229	8180	8645	100
1.82-1.85	0.2186	452	0.2101	8263	8715	100
1.85-1.88	0.2367	447	0.2046	8218	8665	100
1.88-1.91	0.2359	495	0.2102	8221	8716	100
1.91-1.94	0.2479	424	0.2181	8247	8671	100
1.94-1.98	0.2232	430	0.1948	8234	8664	100
1.98-2.02	0.193	511	0.1715	8182	8693	100
2.02-2.06	0.1989	414	0.1651	8244	8658	100
2.06-2.1	0.1896	434	0.1626	8269	8703	100
2.1-2.15	0.1891	399	0.1578	8292	8691	100
2.15-2.2	0.1653	454	0.152	8259	8713	100
2.2-2.26	0.1866	426	0.1571	8254	8680	100
2.26-2.33	0.1805	462	0.1555	8194	8656	100
2.33-2.41	0.1736	454	0.1518	8278	8732	100
2.41-2.49	0.1808	458	0.1551	8250	8708	100
2.49-2.59	0.1831	405	0.1575	8262	8667	100
2.59-2.71	0.1856	445	0.1561	8269	8714	100
2.71-2.85	0.188	409	0.1611	8327	8736	100
2.85-3.03	0.1749	460	0.1555	8210	8670	100
3.03-3.26	0.1712	420	0.1507	8322	8742	100
3.26-3.59	0.1504	464	0.1481	8230	8694	100
3.59-4.11	0.1535	429	0.1378	8320	8749	100
4.11-5.18	0.1478	467	0.1287	8271	8738	100
5.18-49.55	0.1744	412	0.1659	8428	8840	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	1.1373	-0.6114	-0.4334	0.9589	0.114	1.5811	-0.0415	0.0177	0.0491	0.0083	0.0724	-0.1284	-0.0339	0.0766	-0.0235	0.2223	-0.0317	-0.0112	0.2533	-0.0284	0.2334	48.5173	-3.4665	-42.6263
2	1.3821	-0.2177	-0.4416	2.0281	-0.4802	0.5583	-0.0462	0.251	-0.0037	-0.4065	-0.0353	0.0777	0.0435	-0.2058	0.0535	0.2692	-0.0184	-0.0254	0.3104	-0.0241	0.2133	40.1519	0.2975	-53.7037
3	0.6575	-0.3895	-0.3628	1.5537	0.6024	0.7518	-0.0325	0.0002	-0.0325	-0.1678	0.0763	-0.1708	0.0173	0.0985	-0.0138	0.2006	-0.0263	0.0251	0.2941	-0.0248	0.2533	56.3193	-13.241	-51.3967
4	0.6291	0.1472	-0.1531	0.9463	0.2484	2.3603	-0.1225	0.0679	-0.071	-0.1102	0.151	-0.1608	0.1607	0.0932	-0.0114	0.2316	-0.0116	0.0555	0.2993	-0.0382	0.3272	59.6142	-21.6796	-57.6624
5	0.7098	-0.5234	-0.4339	1.8576	0.3692	1.3306	-0.1297	-0.049	-0.0943	0.1479	0.1142	-0.0776	0.2594	0.0067	0.0523	0.2089	-0.0253	0.0225	0.2759	-0.006	0.2573	49.0628	-21.5069	-46.1986
6	1.4881	0.1331	-0.0722	1.7324	0.415	1.1196	-0.0651	-0.0252	-0.1748	0.0185	0.0047	0.2066	0.0863	-0.1452	0.071	0.2006	-0.0035	0.0099	0.2683	-0.0259	0.3	18.2541	-13.629	-40.1101
7	1.5798	-0.7711	-0.6132	2.9818	0.9922	0.4151	0.005	0.4592	-0.1959	-0.73	-0.039	0.1136	-0.1053	-0.1868	0.0669	0.3279	-0.055	0.0179	0.3988	-0.0442	0.2933	33.0927	-17.8172	-50.7471
8	2.0468	0.0205	0.4107	0.8133	0.2237	1.058	0.0244	0.1371	-0.4059	-0.0436	-0.0699	0.4319	0.1491	-0.2545	0.0373	0.2438	-0.0495	0.0059	0.3432	-0.0915	0.5039	7.3745	-23.2507	-48.3354
9	2.1803	0.351	1.1157	1.3224	0.3718	1.4093	-0.055	0.2351	0.0278	-0.2428	-0.0586	0.4872	-0.0694	-0.2093	0.1168	0.2553	-0.0091	-0.0475	0.4149	-0.0824	0.4843	2.2028	-12.2374	-51.4599
10	0.7789	-0.4968	0.0207	1.5477	-0.612	1.1991	-0.0116	-0.0523	0.058	0.029	-0.0164	0.054	-0.2329	-0.0144	0.0286	0.2819	0.0121	-0.0373	0.3088	-0.0381	0.2603	24.0548	14.1019	-48.5472
11	2.0306	0.4917	1.034	1.1746	-0.6862	1.3851	-0.0634	0.5073	-0.1357	-0.4816	0.0696	0.1227	0.1779	0.0048	0.0077	0.3667	0.0064	-0.0479	0.3882	-0.058	0.3452	15.4157	-0.8848	-55.3048
12	0.863	-0.0195	-0.3671	1.0305	-0.3946	1.5323	0.0226	0.0636	0.1419	-0.1363	-0.0052	0.0753	-0.3378	-0.1075	-0.0332	0.3857	0.0323	-0.0766	0.2767	-0.0181	0.2605	23.8531	22.7073	-63.6937
13	2.9217	1.5964	1.711	2.0314	0.9752	2.4035	0.0785	0.3951	-0.1648	-0.179	0.035	-0.1895	-0.1571	0.442	-0.0032	0.4716	-0.0096	-0.0467	0.3769	-0.0068	0.2957	35.674	21.4953	-77.7907
14	1.12	0.1959	-0.1696	0.9286	-0.3671	1.9584	-0.0182	-0.0385	0.1216	0.0014	-0.0395	-0.055	-0.349	0.1974	0.0952	0.3342	-0.0141	-0.0508	0.2654	-0.0133	0.2587	34.4677	19.8499	-57.4701
15	1.2364	-0.2448	0.4833	1.5688	0.2912	0.9616	0.0341	0.1066	0.0768	0.0124	-0.0145	0.0055	-0.08	-0.0462	-0.0075	0.2403	0.0168	0.0276	0.2412	0.0214	0.2337	24.4277	23.7864	-23.4883
16	1.6915	-0.1048	0.0979	1.3773	0.0307	0.2111	-0.0843	-0.2215	0.1263	0.3503	0.0373	-0.0032	-0.0239	-0.0134	0.0232	0.3364	0.0272	-0.0202	0.2506	-0.0011	0.2529	32.4817	21.3828	-11.9765
17	1.6245	-0.3781	-0.2301	0.694	-0.129	0.4244	0.0032	-0.0752	0.1915	0.1146	0.059	0.0296	-0.1762	-0.0679	-0.0702	0.344	0.0625	0.0276	0.2493	0.0152	0.2992	14.5773	35.9536	-15.6006
18	1.8807	-0.6274	-1.3837	2.8306	0.5686	2.0796	-0.1544	-0.4525	0.2357	0.6436	0.0548	0.0732	-0.0607	-0.0723	0.0006	0.4625	0.098	0.0687	0.4051	0.0132	0.3476	4.2597	34.7104	-4.5372
19	1.9	-0.6828	-0.5614	1.078	0.2589	0.9543	-0.0512	-0.1305	-0.0451	0.1804	0.063	0.1922	0.0058	-0.047	0.0238	0.2971	0.0434	0.0425	0.2441	0.0349	0.2869	8.2153	24.3014	-14.8503
20	0.8645	0.5189	-0.5901	1.7893	-0.4889	1.9667	0.0055	-0.0201	-0.0778	-0.0306	-0.0097	-0.0221	0.0657	-0.1864	0.0167	0.2508	-0.0015	0.0022	0.2677	0.0061	0.2509	18.7877	-6.3391	-13.8053
21	0.4769	0.1165	-0.6142	1.9552	-1.2183	1.7959	0.0178	-0.0952	0.087	0.4562	0.0539	0.1652	-0.4557	-0.1512	-0.1188	0.3454	0.0376	0.0441	0.2878	-0.0052	0.2833	13.7844	4.8569	-5.9862
22	1.3402	-0.0384	-0.7252	1.0516	-0.517	2.7575	-0.0495	-0.0281	-0.0907	-0.008	0.0275	0.0573	0.3435	-0.2056	0.0387	0.3022	-0.0558	0.0421	0.2251	-0.0002	0.2674	16.2135	-20.0952	3.8372
23	0.7503	-0.1523	0.0878	0.9903	-0.8825	2.6812	-0.0502	0.0247	-0.0867	-0.0736	-0.0277	-0.0533	0.2853	0.1109	0.1113	0.2924	-0.0052	0.0591	0.2082	-0.0005	0.2798	26.4069	-17.2592	-2.685
24	1.9739	0.0993	0.2603	0.5601	0.2709	1.5161	-0.032	0.0199	-0.0806	0.0966	0.0879	-0.0652	0.0264	0.0477	-0.0363	0.2728	0.001	-0.0089	0.1821	-0.0086	0.2349	46.7401	3.561	-16.932
25	1.7145	0.9728	0.264	1.2056	-0.4998	0.8577	0.0593	-0.4947	-0.0729	0.533	-0.163	-0.0052	-0.125	-0.1389	0.0935	0.4059	-0.0116	0.0153	0.3092	0.0217	0.2471	39.9513	-2.497	-3.2996
26	1.1237	0.4663	0.3274	1.1678	0.5285	0.9659	-0.0443	0.0083	-0.0666	0.1662	0.0828	-0.1284	0.0377	0.1937	-0.0194	0.3049	0.0106	-0.051	0.2608	-0.0059	0.2731	59.6865	10.854	-8.6967
27	1.5402	0.2568	0.9395	2.6624	0.4107	1.6002	-0.122	-0.0323	0.0382	0.3093	0.0776	-0.1886	-0.1606	0.1098	0.0016	0.2927	-0.0066	-0.0646	0.2623	-0.0119	0.2425	65.0164	18.1968	-3.6394
28	1.1571	0.9174	0.5282	1.9577	0.6229	1.2931	-0.0878	0.0593	0.0445	0.0093	0.0806	-0.0813	-0.1191	0.0888	0.048	0.2501	-0.0011	-0.0237	0.2267	0.0054	0.2185	52.7724	17.1496	-14.3819

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 0 through 51 )	A	0 - 51
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 52 through 104 )	A	52 - 104
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 105 through 187 )	A	105 - 187
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 188 through 245 )	A	188 - 245
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 246 through 307 )	A	246 - 307
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 64 )	B	1 - 64
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 65 through 94 )	B	65 - 94
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 95 through 215 )	B	95 - 215
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 216 through 307 )	B	216 - 307
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 64 )	C	1 - 64
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 65 through 94 )	C	65 - 94
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 95 through 231 )	C	95 - 231
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 232 through 254 )	C	232 - 254
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 255 through 307 )	C	255 - 307
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 0 through 51 )	D	0 - 51
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 52 through 112 )	D	52 - 112
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 113 through 208 )	D	113 - 208
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 209 through 245 )	D	209 - 245
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 246 through 307 )	D	246 - 307
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 1 through 63 )	E	1 - 63
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 64 through 128 )	E	64 - 128
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 129 through 245 )	E	129 - 245
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 246 through 307 )	E	246 - 307
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 0 through 64 )	F	0 - 64
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 65 through 114 )	F	65 - 114
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 115 through 187 )	F	115 - 187
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 188 through 254 )	F	188 - 254
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 255 through 307 )	F	255 - 307

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