PDB-7nnf: Crystal structure of Mycobacterium tuberculosis ArgF in apo form.

ID or keywords:

Entry

Database: PDB / ID: 7nnf

Title

Crystal structure of Mycobacterium tuberculosis ArgF in apo form.

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: 1.52 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 24, 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	7nnf.cif.gz	708.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7nnf.ent.gz	588.5 KB	Display	PDB format
PDBx/mmJSON format	7nnf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7nnf_validation.pdf.gz	355.5 KB	Display	wwPDB validaton report
Full document	7nnf_full_validation.pdf.gz	364.5 KB	Display
Data in XML	7nnf_validation.xml.gz	78.5 KB	Display
Data in CIF	7nnf_validation.cif.gz	117.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nn/7nnf ftp://data.pdbj.org/pub/pdb/validation_reports/nn/7nnf	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 7nniC 7nnqC 7nnrC 7nnvC 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	7nov-1 2p2g-1 7nos-2 7nnw-2 7nnv-2 7nnz-2 2p2g-2 7nov-2 7nny-2 7nor-1 7np0-2 7nnw-1 7nnf-2 7nou-2 7np0-1 7nnv-1 7nos-1 7nny-1 2i6u-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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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

200 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
100 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
100 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	91.341, 142.381, 98.278
Angle α, β, γ (deg.)	90.000, 117.360, 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.: 10 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1795 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.85 Å³/Da / Density % sol: 56.82 %
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: I04-1 / Wavelength: 0.9159 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 28, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.9159 Å / Relative weight: 1

Reflection

Resolution: 1.52→81.12 Å / Num. obs: 338738 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC_1/2: 0.994 / R_merge(I) obs: 0.106 / R_pim(I) all: 0.05 / R_rim(I) all: 0.118 / Net I/σ(I): 7.4 / Num. measured all: 1731990 / Scaling rejects: 1

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
1.52-1.61	4.2	1.156	209268	49398	0.449	0.632	1.325	1	100
4.82-81.12	5.3	0.084	57641	10863	0.99	0.04	0.093	17.8	99.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	7.97 Å	81.12 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: 1.52→71.19 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1828	16834	4.97 %
R_work	0.1686	321829	-
obs	0.1693	338663	99.91 %

Solvent computation

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

Displacement parameters

B_iso max: 82.33 Å² / B_iso mean: 30.7571 Å² / B_iso min: 15.06 Å²

Refinement step

Cycle: final / Resolution: 1.52→71.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13548	0	50	1797	15395
B_iso mean	-	-	41.33	41.09	-
Num. residues	-	-	-	-	1807

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.52-1.54	0.3136	600	0.2988	10611	11211
1.54-1.56	0.2887	595	0.2861	10702	11297
1.56-1.58	0.286	599	0.2752	10643	11242
1.58-1.6	0.2761	541	0.2633	10764	11305
1.6-1.62	0.2833	619	0.2679	10688	11307
1.62-1.64	0.2874	576	0.2698	10648	11224
1.64-1.66	0.2688	598	0.2545	10694	11292
1.66-1.69	0.263	531	0.2366	10728	11259
1.69-1.72	0.2423	510	0.22	10756	11266
1.72-1.74	0.2496	566	0.2122	10684	11250
1.74-1.77	0.2126	527	0.1986	10757	11284
1.77-1.81	0.2056	559	0.1806	10715	11274
1.81-1.84	0.2124	537	0.18	10751	11288
1.84-1.88	0.1997	487	0.1715	10773	11260
1.88-1.92	0.2049	595	0.1795	10694	11289
1.92-1.96	0.2036	540	0.1803	10767	11307
1.96-2.01	0.1907	624	0.1822	10670	11294
2.01-2.07	0.1952	592	0.168	10661	11253
2.07-2.13	0.1883	552	0.1654	10725	11277
2.13-2.2	0.1877	504	0.1573	10801	11305
2.2-2.28	0.1854	598	0.1624	10695	11293
2.28-2.37	0.1641	441	0.1594	10813	11254
2.37-2.47	0.1769	537	0.1609	10801	11338
2.47-2.6	0.1752	591	0.1638	10685	11276
2.6-2.77	0.1933	528	0.1653	10769	11297
2.77-2.98	0.1715	556	0.1638	10761	11317
2.98-3.28	0.1709	603	0.1578	10720	11323
3.28-3.76	0.1612	597	0.1516	10703	11300
3.76-4.73	0.1499	587	0.1379	10743	11330
4.73-71.19	0.1651	544	0.1658	10907	11451

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	1.0447	0.5332	-0.539	2.2908	-1.1286	2.7072	-0.0311	0.018	-0.0389	0.0356	-0.0353	-0.0734	0.0637	-0.2932	0.0602	0.1759	-0.0094	-0.0004	0.2188	-0.0039	0.1884	42.2853	10.309	117.4714
2	2.5246	-1.0624	-0.7538	1.6157	-0.1719	0.414	0.0183	-0.477	0.0714	0.6998	0.1382	0.1037	-0.4491	-0.1067	-0.1263	0.5251	0.0642	0.0597	0.3006	0.0195	0.2755	38.3124	27.3071	123.6221
3	0.6232	0.6449	0.0533	1.5121	-1.5326	3.1865	-0.0222	0.0427	0.0637	0.1861	0.0065	0.1056	-0.2152	-0.4538	0.0101	0.2057	0.0007	0.0272	0.2498	-0.0091	0.2029	38.5192	10.7395	125.9293
4	0.9683	0.0455	-0.503	1.002	-0.3438	2.5466	-0.176	0.1355	-0.1261	-0.0949	0.106	0.063	0.4608	-0.45	0.0717	0.2983	-0.1122	0.0485	0.2545	-0.0168	0.2152	36.1734	-4.6858	135.3008
5	1.8134	-0.1191	-0.405	0.2243	-0.7791	3.1244	-0.0973	-0.2822	0.0855	-0.1028	-0.1356	0.0942	-0.1062	0.1144	0.1512	0.2596	-0.0044	0.0526	0.2046	0.0029	0.2415	47.8612	-0.2132	141.7728
6	1.6561	0.1174	-0.0198	1.0784	-0.3717	1.6415	-0.139	-0.0592	-0.1742	-0.0761	-0.1249	-0.1318	0.3821	0.3067	0.2528	0.3065	0.025	0.0632	0.1965	0.0367	0.2553	52.8822	-5.354	138.0814
7	2.243	-0.7417	0.3974	2.0855	-1.251	2.523	-0.0011	-0.0281	-0.021	-0.2196	-0.0131	-0.0123	0.2397	-0.2628	0.0476	0.2158	-0.0358	0.0401	0.206	-0.0153	0.1979	44.4368	6.1842	118.0578
8	1.9676	0.5926	0.4564	0.923	0.2296	1.0755	0.0344	-0.2152	-0.0862	0.1691	-0.0324	-0.017	0.0634	-0.0847	-0.0044	0.1832	0.0077	0.0039	0.1298	0.0008	0.1563	69.594	18.8343	119.6598
9	1.1352	0.385	0.6498	1.1875	0.3525	1.2146	-0.0497	-0.0265	0.0102	0.1249	0.0463	-0.1359	-0.1083	0.079	0.0071	0.2048	0.0011	-0.0178	0.1804	-0.0121	0.1876	84.3838	32.8972	122.6059
10	1.6256	-0.7289	0.0462	1.8841	0.2995	0.7701	-0.0218	-0.024	0.0013	0.1159	0.0438	-0.0076	0.0176	-0.0165	0.0039	0.1845	0.0262	0.0184	0.2039	0.0101	0.1773	47.5701	38.1083	109.1441
11	1.9498	0.8118	0.3542	2.6546	0.517	0.1153	-0.0624	-0.4927	0.1902	0.5185	0.0268	0.015	0.0342	-0.1039	-0.0382	0.3233	0.0817	-0.0386	0.294	-0.0341	0.2509	61.7946	37.1648	120.66
12	1.9165	-0.8554	-0.3473	1.0407	0.1116	0.4721	-0.0704	-0.1825	0.2096	0.1514	0.1355	-0.0613	-0.0889	-0.0283	-0.0513	0.2435	0.062	0.0148	0.2272	-0.0035	0.2085	40.2789	51.2792	116.473
13	1.8353	-0.6569	-0.5589	2.2102	0.4523	1.1722	-0.126	-0.3088	-0.103	0.3848	0.078	0.1865	0.0568	0.0473	0.0377	0.3028	0.0856	0.0908	0.3329	0.0556	0.2622	25.6056	45.1568	123.5865
14	3.5498	-0.1474	-0.9506	1.7522	0.2622	1.5602	-0.0114	0.0945	-0.0076	0.0776	0.0717	-0.0001	0.0503	0.012	-0.0388	0.2098	0.0442	-0.0026	0.1777	0.0117	0.1802	43.0573	38.3411	108.4427
15	1.2175	-0.4558	0.3007	2.1327	-1.1217	2.2352	0.0033	0.0219	-0.0135	-0.0997	-0.058	0.0424	-0.0179	-0.0208	0.055	0.1873	0.0136	-0.0129	0.2193	-0.0263	0.1815	47.3326	30.4372	82.9789
16	2.6003	0.5745	0.7922	1.0922	-0.6283	0.9082	-0.0828	0.5673	-0.1531	-0.6883	0.1455	0.1951	0.3168	-0.0559	0.0218	0.4439	-0.0408	-0.0671	0.3204	-0.0289	0.3234	38.4824	15.6795	76.2824
17	0.805	0.0674	-0.6497	1.0243	-0.8164	2.6036	-0.005	0.0923	0.0734	-0.1498	0.0292	0.0616	-0.1915	-0.1654	-0.0265	0.2725	0.0159	-0.063	0.2122	-0.0091	0.2062	47.592	39.2259	67.7091
18	0.9109	0.236	0.1927	0.6815	-0.3104	1.9022	0.0151	0.037	0.0502	-0.0627	-0.0403	-0.0545	-0.2358	0.3747	0.0484	0.2484	-0.0046	-0.0322	0.2124	-0.0021	0.22	58.5456	36.9131	67.6525
19	1.2751	-0.7107	-0.4963	1.4865	0.3364	0.8451	0.0262	0.1466	0.04	-0.1151	-0.0485	0.0018	-0.1054	-0.063	0.0172	0.1598	-0.0075	-0.0178	0.2077	-0.0107	0.1606	70.1363	13.1784	83.3612
20	0.7009	0.0115	-0.3492	1.126	0.4465	1.3759	-0.0907	-0.0166	-0.0815	-0.0268	0.0998	-0.0842	0.1599	0.0665	-0.0015	0.1636	-0	0.0015	0.2063	-0.0046	0.1928	79.3907	-4.9628	80.112
21	1.5284	0.4053	0.0401	1.8961	0.5162	1.0895	-0.0254	-0.0307	-0.1179	0.0402	0.0021	0.1785	0.0542	-0.0729	0.0325	0.165	0.0083	0.0073	0.2191	-0.009	0.2442	41.8504	2.7115	91.4803
22	1.6562	0.0733	0.0362	1.2171	0.3922	0.5519	-0.0343	0.4384	-0.219	-0.3662	0.0005	-0.0801	0.036	0.0058	0.0311	0.2454	-0.0106	0.028	0.2931	-0.0575	0.2435	53.0475	-3.606	81.4301
23	1.6699	0.1581	0.7867	0.9529	0.2166	1.2731	0.0983	0.084	-0.3875	-0.0038	-0.1285	0.4652	0.1591	-0.2168	0.0133	0.1851	-0.0308	0.0055	0.2644	-0.0877	0.4793	26.8862	-6.795	83.7381
24	1.9052	0.9456	0.6681	1.8718	0.3074	0.6945	-0.2138	0.1945	0.1363	-0.4849	-0.0433	0.6189	-0.2107	-0.1519	0.1918	0.2986	0.0124	-0.1579	0.3982	-0.061	0.5584	19.6918	4.163	75.1369
25	1.9964	0.2324	0.9677	2.1469	0.1252	1.7556	-0.047	-0.0457	-0.0127	0.0886	-0.0083	0.3013	-0.0308	-0.14	0.0648	0.1773	-0.0152	0.0374	0.2417	-0.0354	0.2867	37.523	4.3275	91.7321

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 64 )	A	0 - 64
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 65 through 94 )	A	65 - 94
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 95 through 143 )	A	95 - 143
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 144 through 215 )	A	144 - 215
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 216 through 239 )	A	216 - 239
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 240 through 284 )	A	240 - 284
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 285 through 307 )	A	285 - 307
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 143 )	B	1 - 143
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 144 through 307 )	B	144 - 307
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 0 through 64 )	C	0 - 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 215 )	C	95 - 215
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 216 through 284 )	C	216 - 284
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 285 through 307 )	C	285 - 307
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1 through 64 )	D	1 - 64
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 65 through 94 )	D	65 - 94
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 95 through 231 )	D	95 - 231
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 232 through 307 )	D	232 - 307
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 1 through 143 )	E	1 - 143
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 144 through 307 )	E	144 - 307
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 0 through 64 )	F	0 - 64
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 65 through 114 )	F	65 - 114
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 115 through 215 )	F	115 - 215
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 216 through 284 )	F	216 - 284
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 285 through 307 )	F	285 - 307

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