PDB-6p7u: CRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE SUBUNIT OF ACC (ACCD...

ID or keywords:

Entry

Database: PDB / ID: 6p7u

Title

CRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE SUBUNIT OF ACC (ACCD6) IN COMPLEX WITH INHIBITOR QUIZALOFOP-P FROM MYCOBACTERIUM TUBERCULOSIS

Components

Probable propionyl-CoA carboxylase beta chain 6

Keywords

TRANSFERASE / CROTONASE SUPER FAMILY / CARBOXYLTRANSFERASE / TRANSFERASE-HERBICIDE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

acetyl-CoA carboxytransferase / Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases / fatty acid elongation, saturated fatty acid / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / acetyl-CoA carboxylase activity / peptidoglycan-based cell wall / transferase activity
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.198 Å

Authors

Reddy, M.C.M. / Sacchettini, J.C. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Inhibition of Mycobacterium tuberculosis acetyl-CoA carboxyltransferase(AccD6)d omain of acetyl-coenzyme A carboxylase by quizalofop-p
Authors: Reddy, M.C.M. / Sacchettini, J.C.

History

Deposition	Jun 6, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 10, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	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	6p7u.cif.gz	627.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6p7u.ent.gz	517.8 KB	Display	PDB format
PDBx/mmJSON format	6p7u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6p7u_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	6p7u_full_validation.pdf.gz	1.3 MB	Display
Data in XML	6p7u_validation.xml.gz	65.2 KB	Display
Data in CIF	6p7u_validation.cif.gz	93.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p7/6p7u ftp://data.pdbj.org/pub/pdb/validation_reports/p7/6p7u	HTTPS FTP

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Related structure data

Related structure data	4g2rS S: Starting model for refinement
Similar structure data	6prw-3 6prw-1 6pk2-3 6pk2-1 6tzv-3 6tzv-1 4xnw-d 4fb8-d 5n8u-1 4g2r-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

Deposited unit

A: Probable propionyl-CoA carboxylase beta chain 6

B: Probable propionyl-CoA carboxylase beta chain 6

C: Probable propionyl-CoA carboxylase beta chain 6

D: Probable propionyl-CoA carboxylase beta chain 6

hetero molecules

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

1

A: Probable propionyl-CoA carboxylase beta chain 6

B: Probable propionyl-CoA carboxylase beta chain 6

hetero molecules

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

2

C: Probable propionyl-CoA carboxylase beta chain 6

D: Probable propionyl-CoA carboxylase beta chain 6

hetero molecules

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

Unit cell

Length a, b, c (Å)	149.604, 153.343, 102.863
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Probable propionyl-CoA carboxylase beta chain 6 / PCCase / Propanoyl-CoA:carbon dioxide ligase Mass: 50198.934 Da / Num. of mol.: 4 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: accD6, Rv2247, MTCY427.28 / Plasmid: PET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WQH5, propionyl-CoA carboxylase
#2: Chemical	ChemComp-FTJ / (2R)-2-{4-[(6-chloroquinoxalin-2-yl)oxy]phenoxy}propanoic acid Mass: 344.749 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₁₃ClN₂O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 793 / 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: 2.3 Å³/Da / Density meas: 1.35 Mg/m³ / Density % sol: 47 % Description: Thick, triangular, and plate-like with sharp edges
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M Li2SO4, 0.1 M Tris pH 7, 1 M potassium sodium tartrate PH range: 6.5-7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2013 / Details: MIRRORS
Radiation	Monochromator: DOUBLE-CRYSTAL, SI(111) LIQUID N2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.198→48.762 Å / Num. obs: 117732 / % possible obs: 97.49 % / Redundancy: 7 % / Net I/σ(I): 1.34
Reflection shell	Resolution: 2.198→2.432 Å / Num. unique obs: 117732

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.8_1069	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4G2R

4g2r

Resolution: 2.198→48.762 Å / FOM work R set: 0.8533 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2064	5914	5.02 %
R_work	0.1707	111818	-
obs	0.1725	117732	97.49 %

Solvent computation

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

Displacement parameters

B_iso max: 120.21 Å² / B_iso mean: 33.52 Å² / B_iso min: 5.13 Å²

Refinement step

Cycle: final / Resolution: 2.198→48.762 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12323	0	96	793	13212
B_iso mean	-	-	29.44	37.42	-
Num. residues	-	-	-	-	1688

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	12692
X-RAY DIFFRACTION	f_angle_d	1.108	17280
X-RAY DIFFRACTION	f_chiral_restr	0.074	1978
X-RAY DIFFRACTION	f_plane_restr	0.005	2288
X-RAY DIFFRACTION	f_dihedral_angle_d	15.231	4448

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 (%)
2.1977-2.2227	0.2873	146	0.2102	2626	2772	70
2.2227-2.2489	0.2638	179	0.2181	3091	3270	83
2.2489-2.2763	0.2671	158	0.2219	3366	3524	88
2.2763-2.3051	0.2536	197	0.2043	3490	3687	93
2.3051-2.3354	0.2829	172	0.2069	3666	3838	96
2.3354-2.3674	0.2695	196	0.2021	3686	3882	98
2.3674-2.4012	0.2534	191	0.1952	3786	3977	99
2.4012-2.4371	0.2478	202	0.1962	3735	3937	99
2.4371-2.4752	0.2256	198	0.1971	3814	4012	100
2.4752-2.5157	0.2665	199	0.1913	3769	3968	100
2.5157-2.5591	0.2265	193	0.1937	3800	3993	100
2.5591-2.6056	0.2821	191	0.1966	3807	3998	100
2.6056-2.6558	0.2535	210	0.1953	3747	3957	100
2.6558-2.71	0.2475	193	0.1889	3863	4056	100
2.71-2.7689	0.2366	191	0.1891	3769	3960	100
2.7689-2.8333	0.2355	197	0.1968	3813	4010	100
2.8333-2.9041	0.2558	204	0.2039	3791	3995	100
2.9041-2.9826	0.2593	192	0.1958	3836	4028	100
2.9826-3.0704	0.218	201	0.1987	3818	4019	100
3.0704-3.1695	0.214	195	0.1866	3805	4000	100
3.1695-3.2827	0.224	221	0.1818	3778	3999	100
3.2827-3.4141	0.212	199	0.167	3863	4062	100
3.4141-3.5695	0.1903	205	0.1599	3829	4034	100
3.5695-3.7576	0.1917	183	0.1471	3851	4034	100
3.7576-3.9929	0.186	189	0.1398	3849	4038	100
3.9929-4.3011	0.1559	242	0.1347	3827	4069	100
4.3011-4.7336	0.151	221	0.1255	3841	4062	100
4.7336-5.4178	0.1668	188	0.1443	3924	4112	100
5.4178-6.8228	0.2109	214	0.1709	3920	4134	100
6.8228-48.7738	0.1565	247	0.1651	4058	4305	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	0.0479	0.0576	0.0382	0.0859	0.0078	0.075	-0.084	0.0989	-0.0332	-0.0922	0.0415	0.1981	0.1476	-0.3508	-0.0456	-0.0385	-0.3448	-0.0678	0.2554	-0.0302	0.206	-73.569	20.068	-44.1222
2	0.1067	-0.0558	0.0814	0.0315	-0.0428	0.0617	-0.0103	-0.0652	-0.0713	0.0448	0.1053	0.0757	0.1139	-0.1629	0.009	0.2092	-0.091	0.0583	0.2138	0.0066	0.2473	-67.491	20.4816	-26.4495
3	0.2666	-0.1733	0.073	0.1645	0.0054	0.0836	-0.0545	-0.0876	-0.0765	0.1035	0.0629	0.0901	0.0759	-0.081	0.0004	0.2301	-0.0541	0.0764	0.0977	0.0301	0.1409	-55.0473	17.695	-13.0801
4	0.1064	-0.0097	0.0602	0.0848	0.008	0.1565	-0.0722	-0.0285	-0.0564	0.0352	-0.0074	-0.0002	0.1272	-0.0567	-0.0487	0.1139	-0.018	0.0487	0.028	0.0304	0.0972	-45.8378	23.7946	-22.3566
5	0.0064	0.0039	0.0071	0.0028	0.0022	0.0111	0.0131	-0.0137	-0.071	0.1067	0.0073	-0.0631	-0.0424	0.0073	0	0.4357	-0.0257	-0.1142	0.3982	0.0215	0.4884	-20.3123	14.5345	-5.0178
6	0.0179	-0.0076	-0.0106	0.0464	-0.0154	0.015	0.0216	-0.0134	0.0762	0.1561	-0.0266	-0.0389	-0.1199	-0.02	-0.0015	0.1832	-0.0251	0.0466	0.1681	-0.0153	0.1504	-48.2023	35.1024	-11.6213
7	0.0558	-0.0353	-0.1342	0.1049	0.1468	0.4276	-0.0625	-0.0027	0.0441	0.027	0.0394	-0.0424	-0.0487	0.4272	-0.0044	0.0868	-0.0306	-0.0125	0.1984	0.0389	0.1352	-25.9452	32.685	-37.4702
8	0.1978	-0.0242	0.121	0.0054	-0.0139	0.0775	-0.0457	0.1657	-0.0594	-0.1569	-0.0342	-0.0409	0.1492	0.1001	-0.0062	0.2165	-0.027	0.0138	0.1389	0.0269	0.1449	-40.0072	20.4609	-59.3964
9	0.1603	-0.0193	-0.014	0.0138	-0.0129	0.0562	-0.1556	0.026	-0.0955	-0.0149	-0.0036	0.0229	0.1563	-0.091	-0.0855	0.2604	-0.1621	0.0399	0.1492	-0.0123	0.1706	-56.5515	11.9031	-58.2845
10	0.0115	-0.0261	-0.0005	0.065	0.0013	0.0667	-0.0379	0.0648	0.0113	-0.0981	-0.0026	0.0908	0.0651	-0.1146	-0.0415	0.2411	-0.1132	-0.0796	0.3217	0.0369	0.1503	-53.6734	24.7268	-68.3787
11	0.1687	-0.0909	-0.0619	0.1208	0.1299	0.1457	-0.1032	0.1632	-0.1568	0.0296	-0.0775	-0.0676	0.2005	0.344	-0.1369	0.1164	0.12	0.0379	0.3641	0.0352	0.1593	0.7937	-33.5364	-17.2398
12	0.0064	-0.0172	-0.0071	0.1322	0.081	0.048	-0.0037	-0.035	-0.0027	0.144	-0.0177	-0.0292	0.0283	0.2082	0.0043	0.1266	0.0061	0.0029	0.271	0.0386	0.1379	-3.9503	-24.4702	-3.8473
13	0.0128	0.0115	0.0007	0.012	-0.0015	0.011	-0.0872	-0.0833	0.2063	0.0737	-0.0399	-0.0468	-0.0647	0.0848	-0.0001	0.3369	-0.0513	-0.042	0.2677	0.0171	0.2238	-9.9539	-10.74	10.2384
14	0.032	0.0024	-0.0044	0.0069	0.01	0.0134	-0.0447	0.0054	0.0823	0.0276	-0.0542	-0.0846	-0.0278	0.0941	-0	0.196	-0.0253	-0.0061	0.1437	0.0451	0.1666	-15.2653	-15.1599	0.7907
15	0.1018	-0.0342	0.0103	0.0155	-0.0013	0.002	-0.1927	-0.0094	0.1636	0.1122	0.1232	0.0326	-0.1762	0.0556	-0.0034	0.2495	-0.005	-0.002	0.1316	-0.0056	0.1756	-24.8666	-11.0639	3.1019
16	0.0398	-0.0121	0.0277	0.0518	-0.0114	0.0238	-0.0545	-0.0736	0.0431	0.0103	-0.0207	0.0538	-0.0552	-0.0457	-0.0828	0.3946	0.142	0.0538	0.3157	-0.1131	0.2263	-33.8342	0.5803	14.6151
17	0.0016	-0.0031	0.0026	0.0086	-0.0067	0.0056	-0.0938	-0.0712	-0.0877	0.0227	-0.0055	0.0533	0.0222	-0.0106	0.0001	0.3573	0.0264	0.0578	0.3073	0.0131	0.1465	-21.3965	-24.5623	14.4595
18	0.0774	-0.0585	-0.0326	0.0461	0.0246	0.1086	-0.031	-0.0166	-0.0187	0.141	-0.0052	0.2286	0.0383	-0.1596	0.0006	0.1487	0.0196	0.0463	0.0943	-0.0094	0.2289	-45.7978	-10.3949	-8.6053
19	0.0567	0.0073	0.0136	0.0172	-0.0245	0.0485	0.0294	0.0866	0.0525	-0.0224	-0.0026	0.0312	-0.046	-0.0587	0.0082	0.1727	0.0367	-0.0188	0.0878	-0.0121	0.2136	-40.0404	-11.6215	-26.1564
20	0.0252	0.0243	-0.0073	0.029	-0.0135	0.0169	0.059	0.1545	0.091	-0.0693	-0.0726	0.0591	-0.0721	0.0209	0.0023	0.2694	0.0717	-0.0337	0.2249	0.0629	0.2178	-27.4781	-12.5184	-39.5213
21	0.0112	-0.0157	0.0017	0.0212	0.0013	0.0173	-0.0006	0.0212	0.0242	-0.0346	-0.0559	0.0063	0.0314	0.066	-0	0.1321	0.0204	-0.0207	0.1332	0.0041	0.1629	-25.6917	-16.0792	-28.5691
22	0.0466	-0.0491	0.0107	0.056	-0.0149	0.0302	0.0398	0.1426	0.0878	-0.0009	-0.0036	-0.1038	-0.1186	0.1603	0.0002	0.1403	0.0284	-0.0015	0.2126	0.0061	0.1658	-15.1237	-20.8901	-31.1329
23	0.0031	0.0014	-0.001	0.0021	0.0019	0.0043	-0.0431	0.0032	0.0428	-0.0287	-0.0366	-0.0182	-0.0189	-0.0198	-0.0001	0.6431	0.075	0.1359	0.8827	0.0707	0.7094	8.8404	-14.6116	-46.5181
24	0.0007	-0.0004	-0.0006	0.0082	0.0042	0.0018	0.063	0.1015	-0.026	-0.0694	-0.008	-0.0498	0.072	0.1067	0.0282	0.2492	0.1174	-0.0198	0.2857	-0.0515	0.1191	-21.8248	-30.3732	-40.2278

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 13 through 145 )	A	13 - 145
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 146 through 226 )	A	146 - 226
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 227 through 268 )	A	227 - 268
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 269 through 401 )	A	269 - 401
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 402 through 428 )	A	402 - 428
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 429 through 466 )	A	429 - 466
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 13 through 213 )	B	13 - 213
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 214 through 312 )	B	214 - 312
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 313 through 425 )	B	313 - 425
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 426 through 466 )	B	426 - 466
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 13 through 121 )	C	13 - 121
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 122 through 226 )	C	122 - 226
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 227 through 268 )	C	227 - 268
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 269 through 313 )	C	269 - 313
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 314 through 393 )	C	314 - 393
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 394 through 446 )	C	394 - 446
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 447 through 466 )	C	447 - 466
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 13 through 145 )	D	13 - 145
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 146 through 226 )	D	146 - 226
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 227 through 268 )	D	227 - 268
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 269 through 313 )	D	269 - 313
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 314 through 401 )	D	314 - 401
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 402 through 426 )	D	402 - 426
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 427 through 466 )	D	427 - 466

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Yorodumi