PDB-4c6z: Crystal structure of M. tuberculosis C171Q KasA in complex with TLM3

ID or keywords:

Entry

Database: PDB / ID: 4c6z

Title

Crystal structure of M. tuberculosis C171Q KasA in complex with TLM3

Components

3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1

Keywords

TRANSFERASE / BETO-KETOACYL-ACP SYNTHASE / KAS ENZYME / CONDENSING ENZYME / TYPE 2 FATTY ACID BIOSYNTHESIS / MYCOLIC ACID SYNTHESIS / THIOLACTOMYCIN

Function / homology

Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / : / Chem-M7U / Chem-TLE / :

Function and homology information

Biological species

MYCOBACTERIUM TUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Schiebel, J. / Kapilashrami, K. / Fekete, A. / Bommineni, G.R. / Schaefer, C.M. / Mueller, M.J. / Tonge, P.J. / Kisker, C.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for the Recognition of Mycolic Acid Precursors by Kasa, a Condensing Enzyme and Drug Target from Mycobacterium Tuberculosis
Authors: Schiebel, J. / Kapilashrami, K. / Fekete, A. / Bommineni, G.R. / Schaefer, C.M. / Mueller, M.J. / Tonge, P.J. / Kisker, C.

History

Deposition	Sep 19, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2013	Group: Database references
Revision 1.2	Oct 23, 2013	Group: Database references
Revision 1.3	Dec 11, 2013	Group: Database references
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4c6z.cif.gz	341.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4c6z.ent.gz	277.7 KB	Display	PDB format
PDBx/mmJSON format	4c6z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4c6z_validation.pdf.gz	878.1 KB	Display	wwPDB validaton report
Full document	4c6z_full_validation.pdf.gz	887.1 KB	Display
Data in XML	4c6z_validation.xml.gz	41.2 KB	Display
Data in CIF	4c6z_validation.cif.gz	62.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c6/4c6z ftp://data.pdbj.org/pub/pdb/validation_reports/c6/4c6z	HTTPS FTP

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Related structure data

Related structure data	4c6uC 4c6vC 4c6wC 4c6xC 4c70C 4c71C 4c72C 4c73C 2wggS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6y2i-d 2wgg-2 2wgg-4 3sqz-2 4c70-d 4jrm-1 6y2j-3 2wge-1 2vb9-1 4c73-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1

B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	74.700, 89.340, 183.480
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1 / BETA-KETOACYL ACP SYNTHASE Mass: 45845.676 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PFPCA1 / Production host: MYCOBACTERIUM SMEGMATIS (bacteria) / Strain (production host): MC2155 References: UniProt: I6Y8T4, beta-ketoacyl-[acyl-carrier-protein] synthase I

#1: Protein

3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1 / BETA-KETOACYL ACP SYNTHASE

Mass: 45845.676 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PFPCA1 / Production host:

MYCOBACTERIUM SMEGMATIS (bacteria) / Strain (production host): MC2155
References: UniProt: I6Y8T4, beta-ketoacyl-[acyl-carrier-protein] synthase I

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Non-polymers , 5 types, 874 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-TLE / (5R)-3-ethyl-4-hydroxy-5-methyl-5-[(1E)-2-methylbuta-1,3-dien-1-yl]thiophen-2(5H)-one Mass: 224.319 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₁₆O₂S
#5: Chemical	ChemComp-M7U / (2R)-2-(hexadecanoyloxy)-3-{[(10R)-10-methyloctadecanoyl]oxy}propyl phosphate Mass: 690.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₈H₇₅O₈P
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 859 / 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: 3.53 Å³/Da / Density % sol: 65.19 % / Description: NONE
Crystal grow	pH: 9.5 / Details: 20% PEG 3350, pH 9.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
Detector	Type: MARRESEARCH / Detector: CCD / Date: Jun 10, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.8→36.07 Å / Num. obs: 114325 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 4.1 % / R_merge(I) obs: 0.1 / Net I/σ(I): 9.1
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 4 % / R_merge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2WGG

2wgg

Resolution: 1.8→91.74 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.942 / SU B: 4.521 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19622	5713	5 %	RANDOM
R_work	0.16042	-	-	-
obs	0.16223	108351	99.74 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 25.925 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.19 Å²	0 Å²	0 Å²
2-	-	1.63 Å²	0 Å²
3-	-	-	-1.44 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→91.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6054	0	162	859	7075

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	6579
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.641	1.976	8952
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.501	5	900
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.481	23.606	269
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.357	15	1021
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.828	15	53
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	987
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.021	5099
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.455	1.5	4220
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.083	2	6757
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.7	3	2359
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.469	4.5	2160
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	429	-
R_work	0.254	7918	-
obs	-	-	99.83 %

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	0.9437	0.0803	0.0323	0.6488	0.0688	0.5275	0.0068	0.0565	-0.1416	-0.0515	-0.0194	-0.0935	0.1418	0.0933	0.0126	0.0877	0.0254	0.0132	0.0494	0.0272	0.0707	6.7695	-33.1474	10.4104
2	0.5629	0.4104	-0.5033	0.7495	-1.4892	3.2758	-0.0424	-0.0518	-0.1604	-0.1251	-0.1074	-0.1221	0.3335	0.1795	0.1498	0.1963	0.0159	0.0112	0.0884	0.0408	0.1264	2.1927	-43.8964	25.7022
3	2.1188	0.8704	-0.153	1.865	0.4274	0.4961	-0.0082	-0.2131	-0.1955	0.0887	0.0002	-0.2219	0.1735	0.1286	0.0081	0.1502	0.0504	-0.011	0.1475	0.0376	0.1245	12.9374	-33.7928	26.8702
4	1.1794	0.5398	0.2134	0.5146	0.1425	0.6999	0.0232	-0.0738	-0.0309	0.0302	-0.021	0.0185	0.1307	0.0066	-0.0022	0.1337	0.0018	-0.014	0.0663	0.0194	0.088	-4.0095	-33.1809	31.9501
5	0.0801	0.0966	-0.0977	0.4371	0.129	0.472	0.0024	-0.0208	-0.003	-0.0466	-0.0132	-0.1021	0.081	0.0064	0.0108	0.1221	0.0137	0.0144	0.1148	0.0046	0.1222	3.7216	-19.2212	23.6385
6	0.389	0.005	-0.1128	0.3872	-0.0621	0.4844	-0.0016	0.0544	-0.0129	-0.0682	-0.0311	0.0051	0.0804	-0.0024	0.0326	0.104	0.0177	0.0052	0.0717	0.0072	0.0812	0.3373	-28.482	9.6912
7	4.0257	-1.9441	3.3475	3.1215	-0.7204	7.7799	0.0826	0.1279	-0.0339	0.0838	-0.0413	-0.289	0.0918	0.6419	-0.0414	0.0122	-0.0076	-0.0023	0.208	0.0444	0.1721	23.758	-19.6819	22.0723
8	0.7561	-0.1543	-0.0749	0.4883	0.0577	0.5432	0.0205	0.0726	0.0606	-0.0777	-0.0438	-0.0505	-0.0058	0.0414	0.0233	0.0995	0.0118	0.0142	0.091	0.0253	0.0882	4.5254	-16.7688	5.7929
9	1.2844	-0.0638	-0.4913	0.4281	0.4485	0.9193	0.018	0.0518	0.0127	-0.0937	0.0009	-0.0509	-0.0459	0.067	-0.0189	0.0929	0.0191	0.0285	0.092	0.0418	0.0926	9.7369	-19.7183	2.0209
10	0.74	0.1163	0.1332	0.916	-0.211	0.8184	-0.0127	-0.0851	0.0579	0.0745	-0.0041	0.1828	-0.0527	-0.223	0.0168	0.0498	-0.0014	0.034	0.0948	-0.0334	0.0697	-19.1752	-14.3601	39.4358
11	0.3355	-0.3029	-1.3495	3.5118	2.0375	5.7686	0.012	0.1792	-0.0419	-0.2525	-0.2469	0.4451	-0.1904	-0.8437	0.2349	0.0688	0.017	-0.0362	0.2388	-0.0309	0.145	-27.1546	-18.8209	23.3871
12	0.9908	0.8185	-0.3664	3.4271	-0.7546	1.4498	0.0852	-0.0123	0.1635	-0.1204	-0.1105	0.2984	-0.1428	-0.145	0.0253	0.0821	0.039	-0.008	0.1104	-0.0079	0.1027	-19.221	-6.3903	23.5574
13	0.1447	0.1868	0.0473	1.3953	0.258	0.4116	0.0224	0.0154	0.0331	0.0005	0.0122	0.0912	0.0114	-0.0993	-0.0345	0.0953	0.0003	-0.0117	0.0844	0.0121	0.1065	-15.3658	-22.3883	17.455
14	0.4774	-0.1892	0.3787	1.14	-0.8216	1.0343	0.0119	0.0108	0.0896	-0.0489	-0.0403	0.0314	0.136	0.049	0.0283	0.1098	0.0124	-0.0012	0.0829	-0.0021	0.105	-3.997	-13.5095	28.2811
15	0.3155	0.0344	0.1511	0.8775	-0.2782	0.701	0.0189	-0.1042	0.0021	0.0891	-0.0539	0.0688	0.0161	-0.0968	0.035	0.1005	-0.017	0.0284	0.091	-0.0147	0.0745	-13.6931	-19.9228	40.3455
16	4.3627	0.0508	0.9928	2.5564	-1.4179	6.6932	-0.0428	0.0109	0.3515	0.1027	-0.068	0.0038	-0.4287	-0.2326	0.1108	0.1758	0.0226	-0.023	0.0282	-0.0394	0.1428	-7.9041	5.9651	31.2216
17	0.4002	-0.0683	-0.0385	0.5171	0.1536	0.6205	-0.0165	-0.0888	0.052	0.1533	-0.0323	-0.021	0.0077	-0.0219	0.0488	0.1329	-0.0096	-0.0014	0.0785	-0.0116	0.0719	-3.4647	-13.8601	45.9137
18	0.6465	-0.0681	-0.0529	1.1314	-0.1799	0.8668	0.026	-0.1231	0.0662	0.1491	-0.0502	0.0422	-0.1089	-0.0223	0.0242	0.1326	-0.0134	0.0048	0.0776	-0.0391	0.077	-7.1469	-9.9708	49.4969

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 63
2	X-RAY DIFFRACTION	2	A	64 - 82
3	X-RAY DIFFRACTION	3	A	83 - 102
4	X-RAY DIFFRACTION	4	A	103 - 160
5	X-RAY DIFFRACTION	5	A	161 - 183
6	X-RAY DIFFRACTION	6	A	184 - 251
7	X-RAY DIFFRACTION	7	A	252 - 266
8	X-RAY DIFFRACTION	8	A	267 - 372
9	X-RAY DIFFRACTION	9	A	373 - 416
10	X-RAY DIFFRACTION	10	B	4 - 63
11	X-RAY DIFFRACTION	11	B	64 - 82
12	X-RAY DIFFRACTION	12	B	83 - 102
13	X-RAY DIFFRACTION	13	B	103 - 160
14	X-RAY DIFFRACTION	14	B	161 - 183
15	X-RAY DIFFRACTION	15	B	184 - 251
16	X-RAY DIFFRACTION	16	B	252 - 266
17	X-RAY DIFFRACTION	17	B	267 - 372
18	X-RAY DIFFRACTION	18	B	373 - 416

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 874 molecules

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