PDB-7nnc: Crystal structure of Mycobacterium tuberculosis ArgD with prosthe...

ID or keywords:

Entry

Database: PDB / ID: 7nnc

Title

Crystal structure of Mycobacterium tuberculosis ArgD with prosthetic group pyridoxal-5'-phosphate and 6-Methoxyquinoline-3-carboxylic acid

Components

Acetylornithine aminotransferase

Keywords

TRANSFERASE / ArgD / N-acetylornithine aminotrasferase /

AcOAT

Function / homology

Function and homology information

acetylornithine transaminase /

N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / arginine biosynthetic process /

pyridoxal phosphate binding / identical protein binding /

cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.7 Å

Authors

Gupta, P. / Mendes, V. / 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	7nnc.cif.gz	599.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7nnc.ent.gz	487.7 KB	Display	PDB format
PDBx/mmJSON format	7nnc.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/nn/7nnc ftp://data.pdbj.org/pub/pdb/validation_reports/nn/7nnc	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 7nnfC 7nniC 7nnqC 7nnrC 7nnvC 7nnwC 7nnyC 7nnzC 7norC 7nosC 7notC 7nouC 7novC 7np0C 7nphC 7npjC 4adbS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7nnc-2 6v8d-2 6v8c-1 2byj-1 1wkg-d 7nn1-2 7jx9-1 2byj-2 7nn1-1 7jx9-2 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

Deposited unit

A: Acetylornithine aminotransferase

B: Acetylornithine aminotransferase

C: Acetylornithine aminotransferase

D: Acetylornithine aminotransferase

hetero molecules

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

1

A: Acetylornithine aminotransferase

B: Acetylornithine aminotransferase

hetero molecules

defined by author&software
Evidence: gel filtration
82.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Acetylornithine aminotransferase

D: Acetylornithine aminotransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.461, 184.944, 71.578
Angle α, β, γ (deg.)	90.000, 106.060, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Acetylornithine aminotransferase / ACOAT Mass: 41325.035 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: argD, Rv1655, MTCY06H11.20 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WPZ7, acetylornithine transaminase
#2: Chemical	ChemComp-NO3 / NITRATE ION / Nitrate Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO₃
#3: Chemical	ChemComp-UMH / 6-methoxyquinoline-3-carboxylic acid Mass: 203.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₉NO₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1607 / 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: 2.52 Å³/Da / Density % sol: 51.17 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Bis-Tris Propane pH 8.5 18% PEG Smear High (PEGs 6K, 8K, 10K) 0.2 M ammonium nitrate 10 mM nickel chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.97625 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 30, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.97625 Å / Relative weight: 1

Reflection

Resolution: 1.7→68.78 Å / Num. obs: 177420 / % possible obs: 99.3 % / Redundancy: 5.3 % / CC_1/2: 0.999 / R_merge(I) obs: 0.029 / R_pim(I) all: 0.014 / R_rim(I) all: 0.033 / Net I/σ(I): 34 / Num. measured all: 948793

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
1.7-1.73	4.9	0.089	41174	8457	0.994	0.044	0.1	12.1	95.6
9.31-68.78	5	0.029	5314	1071	0.998	0.014	0.032	58.9	96.3

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	5.93 Å	55.19 Å
Translation	5.93 Å	55.19 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
Aimless	0.7.4	data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ADB

4adb

Resolution: 1.7→68.78 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 15.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1622	8907	5.02 %
R_work	0.1455	168461	-
obs	0.1463	177368	99.24 %

Solvent computation

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

Displacement parameters

B_iso max: 62.48 Å² / B_iso mean: 22.79 Å² / B_iso min: 8.33 Å²

Refinement step

Cycle: final / Resolution: 1.7→68.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11324	0	23	1609	12956
B_iso mean	-	-	36.24	33.74	-
Num. residues	-	-	-	-	1564

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.7-1.72	0.1851	289	0.1527	5417	95
1.72-1.74	0.1866	261	0.146	5424	96
1.74-1.76	0.1796	296	0.1421	5511	97
1.76-1.78	0.1771	310	0.144	5546	98
1.78-1.81	0.1667	316	0.1405	5537	99
1.81-1.83	0.167	312	0.1431	5615	99
1.83-1.86	0.1658	306	0.1392	5604	99
1.86-1.89	0.17	317	0.1382	5653	99
1.89-1.91	0.1744	280	0.1407	5565	99
1.91-1.95	0.1734	284	0.1425	5634	99
1.95-1.98	0.1771	307	0.1448	5651	100
1.98-2.02	0.1812	316	0.1459	5561	100
2.02-2.05	0.1668	317	0.1469	5624	100
2.05-2.1	0.1654	300	0.1445	5630	100
2.1-2.14	0.1731	275	0.143	5631	100
2.14-2.19	0.1537	295	0.14	5660	100
2.19-2.25	0.1722	282	0.145	5678	100
2.25-2.31	0.1806	324	0.1435	5613	100
2.31-2.38	0.178	308	0.1466	5602	100
2.38-2.45	0.1795	297	0.1547	5652	100
2.45-2.54	0.1731	294	0.1507	5667	100
2.54-2.64	0.1688	284	0.152	5670	100
2.64-2.76	0.1777	300	0.159	5659	100
2.76-2.91	0.1621	282	0.1519	5646	100
2.91-3.09	0.1547	294	0.1497	5649	100
3.09-3.33	0.1591	307	0.1466	5648	100
3.33-3.66	0.1438	314	0.1425	5642	100
3.66-4.19	0.1408	287	0.1307	5687	100
4.19-5.28	0.1427	247	0.132	5720	100
5.28-68.78	0.1559	306	0.1559	5665	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	0.241	-0.1931	-0.0457	1.3779	-0.0719	0.4962	-0.1096	-0.0505	0.1242	0.102	0.0416	-0.2617	-0.2223	0.1837	0.0706	0.2259	-0.0662	-0.0546	0.2001	-0.0002	0.1745	33.0519	45.6594	33.7355
2	0.8418	0.7221	0.1385	1.6912	-0.5105	0.5947	-0.0313	-0.1752	-0.0172	0.3095	-0.0003	0.1524	-0.2018	0.0474	0.0422	0.204	0.0339	0.0372	0.2053	0.0182	0.1449	12.9505	31.5761	45.4388
3	0.4341	-0.1712	0.2042	1.2353	-0.2162	1.5249	-0.0161	-0.0151	-0.0507	-0.0772	0.0661	0.227	-0.023	-0.0674	-0.0421	0.1099	0.0056	-0.0199	0.1072	0.0249	0.1494	7.9464	32.8333	22.9827
4	1.0187	-0.8654	0.3246	1.2753	-0.6716	0.7728	0.1151	0.17	-0.0378	-0.331	-0.0911	0.0886	0.0594	0.1785	-0.0242	0.2446	-0.0016	-0.0196	0.1837	-0.0031	0.1335	17.6364	35.159	8.5734
5	0.2719	-0.1461	0.085	0.9099	-0.2837	0.8714	-0.0519	-0.0241	-0.0045	-0.0444	0.0623	0.1805	-0.1339	-0.0677	-0.0096	0.1426	0.0075	-0.0207	0.1255	0.0125	0.1587	7.8195	39.4693	22.8436
6	0.5201	0.4955	0.2375	1.1256	-0.5652	1.0675	-0.2716	0.3398	0.3722	-0.2657	0.1546	0.2286	-0.4704	-0.1371	0.0238	0.4046	-0.0747	-0.0958	0.1741	0.0534	0.208	18.505	61.2148	20.4796
7	0.5622	0.3161	0.2274	0.9041	-0.1165	0.8751	-0.1621	0.0719	0.0875	-0.0135	0.0463	-0.2181	-0.2886	0.2551	0.0952	0.3248	-0.1011	-0.0648	0.1811	0.0256	0.1908	27.9005	58.3988	25.2088
8	0.9648	-0.1143	0.0685	1.089	-0.01	0.5921	-0.0583	-0.136	-0.1346	0.1195	0.2081	0.5389	0.017	-0.3719	-0.0459	0.1471	0.028	0.0725	0.2284	0.0823	0.3019	-0.2728	23.9227	37.8272
9	0.3497	-0.1678	0.1309	0.5056	-0.2641	0.4977	-0.0889	-0.2013	-0.0728	0.2895	0.0875	0.0543	-0.1818	-0.0631	0.013	0.1723	0.0402	0.0478	0.1888	0.0312	0.1123	19.1756	28.3128	45.9631
10	1.4075	-0.2942	0.4636	1.8407	-0.3962	1.54	-0.0722	-0.0123	-0.0139	0.1447	-0.0261	-0.3318	-0.0649	0.2116	0.0465	0.1219	-0.018	-0.0077	0.1855	0.0102	0.1737	37.3042	27.8545	33.1166
11	0.6655	-0.2795	0.2568	1.5573	-0.0803	0.9393	-0.0085	0.1083	-0.0706	-0.155	-0.0241	0.1095	0.0074	0.024	0.0346	0.1475	0.0044	0.0062	0.1577	-0.003	0.1339	25.7363	19.1393	19.3623
12	1.5087	-0.6226	0.2753	1.5014	-0.0027	0.6493	0.063	0.2103	-0.1948	-0.2729	-0.0722	0.0473	0.0322	0.1092	0.0243	0.2018	0.0037	0.0014	0.1728	-0.0324	0.1933	20.5716	11.9839	17.645
13	1.0888	0.1254	0.0292	1.5274	-0.615	1.3827	-0.0484	0.1496	-0.2347	-0.2375	-0.0162	-0.0103	0.214	0.0771	0.0526	0.1449	0.0379	0.0406	0.184	-0.0095	0.1679	31.9077	9.4105	22.6522
14	0.1963	0.1067	-0.0594	0.4132	-0.5222	1.3662	-0.0485	-0.0224	-0.1495	-0.0096	-0.0177	-0.0549	0.0606	0.1812	0.052	0.139	0.0259	0.0304	0.198	0.0312	0.1817	33.0164	14.8094	34.297
15	0.4984	-0.0527	0.1747	0.7498	-0.0045	0.5818	-0.0653	-0.0579	-0.0292	0.055	0.0266	-0.0812	-0.1546	0.0971	0.0468	0.1319	-0.0038	0.0068	0.1823	0.0137	0.1265	30.2013	28.29	33.8959
16	1.6848	0.721	-0.029	0.9009	-0.1057	0.5083	-0.3713	-0.0753	-1.0438	0.0006	0.2036	-0.2132	0.4635	0.1046	0.0088	0.1878	0.0906	0.1194	0.1783	0.1248	0.4563	21.8692	1.7041	44.117
17	0.1959	-0.0106	-0.4736	0.8378	0.612	1.573	-0.2216	-0.0366	-0.3648	-0.0283	0.027	0.3259	0.0561	-0.4409	0.03	0.1365	0.0066	0.112	0.2656	0.0797	0.2715	7.8086	8.082	43.4565
18	0.5552	0.0562	-0.2405	0.2161	-0.0788	1.0997	-0.237	-0.2706	-0.7108	0.1649	0.1422	0.229	0.3018	-0.1001	0.0538	0.1269	0.0085	0.2429	0.2162	0.2012	0.335	14.8691	5.5911	47.7206
19	1.0664	-0.1078	0.0688	1.0916	-0.5231	1.0562	0.0555	0.3334	-0.2836	-0.5158	-0.0421	-0.1751	0.1741	0.0864	-0.0261	0.2389	0.024	0.0275	0.2216	-0.0737	0.1914	12.013	-21.9047	-15.8154
20	0.4945	-0.1484	-0.0942	1.2104	0.1428	0.5748	0.0474	-0.0211	-0.1485	0.0533	0.0426	0.1547	0.115	-0.0828	-0.0842	0.1224	-0.0145	-0.0236	0.1513	0.0321	0.1593	-4.1046	-22.5024	5.0266
21	0.7625	-0.2249	0.1311	1.2348	-0.4705	0.8428	0.03	-0.0069	-0.0535	0.2208	-0.026	-0.2065	0.0017	0.1076	-0.0248	0.1712	-0.0044	-0.0682	0.1443	0.0131	0.1684	18.9068	-18.8035	17.4572
22	0.7269	0.0433	0.0963	0.8145	-0.0808	0.4228	0.0484	-0.0829	-0.143	0.1194	0.0437	-0.0146	0.0703	-0.0411	-0.0866	0.1729	-0.0017	-0.0357	0.1514	0.03	0.1413	4.6495	-23.5297	16.1208
23	0.6091	0.0024	0.2005	1.4844	0.415	0.9081	0.1007	0.0205	-0.2464	0.0794	0.1358	-0.2068	0.2878	0.105	-0.1773	0.1786	0.0197	-0.085	0.1435	-0.0206	0.2254	8.5777	-35.9289	4.3144
24	0.134	-0.0068	0.0844	1.3722	-0.2781	1.1538	-0.0284	-0.2497	-0.0565	0.4127	0.1395	0.4152	-0.0895	-0.297	-0.0958	0.222	0.0453	0.0852	0.2456	0.0444	0.2067	-10.0516	-6.791	19.4539
25	0.7633	-0.2191	-0.0116	0.7865	-0.0185	0.6472	0.063	0.0515	-0.0533	-0.0918	0.0425	0.1555	-0.0027	-0.1282	-0.0877	0.1001	-0.0049	-0.0091	0.1462	0.0234	0.1166	-4.4508	-10.7985	-5.9481
26	0.8031	-0.0047	-0.0596	1.0601	-0.4308	1.179	0.0339	0.0341	0.0864	0.089	-0.0232	-0.1386	-0.1478	0.067	-0.0083	0.119	-0.0179	0.0036	0.1259	0.0066	0.137	16.029	4.458	0.6295
27	1.1599	0.0103	-0.3109	0.6433	-0.1331	0.8525	0.1259	0.0559	0.2196	-0.0144	0.0332	0.0602	-0.2136	-0.1226	-0.1407	0.1368	0.0253	0.0392	0.1455	0.0336	0.1418	-3.9771	4.4008	-3.2433

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 7 through 62 )	A	7 - 62
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 63 through 85 )	A	63 - 85
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 86 through 143 )	A	86 - 143
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 144 through 180 )	A	144 - 180
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 181 through 306 )	A	181 - 306
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 307 through 346 )	A	307 - 346
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 347 through 397 )	A	347 - 397
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 7 through 29 )	B	7 - 29
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 30 through 85 )	B	30 - 85
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 86 through 112 )	B	86 - 112
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 113 through 143 )	B	113 - 143
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 144 through 180 )	B	144 - 180
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 181 through 224 )	B	181 - 224
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 225 through 251 )	B	225 - 251
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 252 through 304 )	B	252 - 304
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 305 through 346 )	B	305 - 346
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 347 through 365 )	B	347 - 365
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 366 through 397 )	B	366 - 397
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 7 through 29 )	C	7 - 29
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 30 through 112 )	C	30 - 112
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 113 through 224 )	C	113 - 224
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 225 through 272 )	C	225 - 272
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 273 through 397 )	C	273 - 397
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 7 through 29 )	D	7 - 29
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 30 through 112 )	D	30 - 112
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 113 through 224 )	D	113 - 224
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 225 through 397 )	D	225 - 397

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Version 3 of the EMDB header file is now the official format.
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