PDB-4c73: Crystal structure of M. tuberculosis C171Q KasA in complex with TLM6

ID or keywords:

Entry

Database: PDB / ID: 4c73

Title

Crystal structure of M. tuberculosis C171Q KasA in complex with TLM6

Components

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

Keywords

TRANSFERASE / 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-TLH / :

Function and homology information

Biological species

MYCOBACTERIUM TUBERCULOSIS H37RV (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	4c73.cif.gz	344.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4c73.ent.gz	280.6 KB	Display	PDB format
PDBx/mmJSON format	4c73.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4c73_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4c73_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4c73_validation.xml.gz	41 KB	Display
Data in CIF	4c73_validation.cif.gz	61.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c7/4c73 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/4c73	HTTPS FTP

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Related structure data

Related structure data	4c6uC 4c6vC 4c6wC 4c6xC 4c6zC 4c70C 4c71C 4c72C 2wggS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4c6x-d 4c71-d 2wgf-1 6y2j-4 2wgf-4 2wgd-1 2wgg-2 2wgg-4 2wgg-1 6p9m-1 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

94.9 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)	74.470, 89.130, 183.780
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 H37RV (bacteria) 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 H37RV (bacteria)
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, 760 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 19 / 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-TLH / (5R)-5-methyl-5-[(1E)-2-methylbuta-1,3-dienyl]-4-oxidanyl-3-[2,2,2-tris(fluoranyl)ethanoyl]thiophen-2-one Mass: 292.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₁₁F₃O₃S
#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.: 735 / 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: 3.52 Å³/Da / Density % sol: 65.06 % / Description: NONE
Crystal grow	pH: 7.5 / Details: 0.1 M TRIS PH 7.5, 15% PEG 6000

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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→36.04 Å / Num. obs: 113933 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 4.1 % / R_merge(I) obs: 0.1 / Net I/σ(I): 10.2
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.59 / Mean I/σ(I) obs: 2.3 / % 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: PDB ENTRY 2WGG

2wgg

Resolution: 1.8→91.89 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.959 / SU B: 3.957 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17311	5695	5 %	RANDOM
R_work	0.14468	-	-	-
obs	0.14611	108035	99.82 %	-

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: 20.038 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.37 Å²	0 Å²	0 Å²
2-	-	1.72 Å²	0 Å²
3-	-	-	-1.35 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→91.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6054	0	210	735	6999

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	6673
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.73	1.98	9073
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.518	5	910
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.55	23.7	273
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.975	15	1032
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.873	15	53
X-RAY DIFFRACTION	r_chiral_restr	0.121	0.2	999
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.021	5167
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	1.447	1.5	4258
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.115	2	6824
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.812	3	2415
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.882	4.5	2215
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	0.297	451	-
R_work	0.27	7879	-
obs	-	-	99.89 %

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	1.1785	0.0129	-0.1238	0.3752	-0.1072	0.6148	-0.058	0.0563	-0.195	-0.0053	0.0292	-0.074	0.1304	0.1026	0.0287	0.1086	0.0206	0.009	0.0792	0.0113	0.1185	6.25	-33.3801	10.419
2	0.4133	0.5199	-0.5967	0.8441	-1.1666	1.8254	-0.0314	-0.0944	-0.2063	-0.1155	-0.1234	-0.1857	0.3252	0.1581	0.1548	0.258	0.0459	0.0216	0.1073	0.056	0.1714	2.184	-43.6215	25.6952
3	4.3446	1.9048	0.3065	1.7382	0.3366	1.041	0.0447	-0.1583	-0.3313	0.1677	-0.0166	-0.232	0.2597	0.2856	-0.0281	0.1459	0.065	-0.0313	0.1609	0.0364	0.1269	12.9092	-33.416	26.998
4	1.326	0.6236	-0.0837	0.5157	0.059	0.7887	0.0274	-0.1004	-0.0456	0.1156	-0.0094	0.0311	0.1626	0.0287	-0.0179	0.162	0.0067	-0.0036	0.0906	0.0216	0.1232	-4.1442	-32.83	31.7765
5	0.3665	0.2621	0.1668	0.5935	-0.0339	1.397	-0.0277	-0.1056	0.0658	0.0397	-0.0012	-0.0488	-0.0787	-0.0326	0.0289	0.096	0.021	-0.0092	0.1093	-0.0054	0.127	3.5029	-19.0057	23.3723
6	0.8412	0.1115	-0.1295	0.4781	-0.1193	0.5648	-0.0419	0.0718	-0.0585	-0.0459	0.0214	-0.0133	0.0428	-0.0152	0.0205	0.0985	0.0119	0.0038	0.0962	0.0007	0.0991	0.0792	-28.5161	9.655
7	1.9143	-1.0356	-0.0888	2.0067	-0.4722	4.8796	0.0223	0.0033	0.0641	0.1316	-0.0911	-0.2462	-0.0465	0.6904	0.0688	0.0332	-0.0287	-0.0402	0.2378	0.0142	0.1708	23.5316	-19.4352	21.9266
8	0.9286	-0.1975	-0.3373	0.5308	0.0505	0.6578	-0.0034	0.1048	0.1097	-0.0376	-0.0107	-0.0554	-0.0626	0.0373	0.0141	0.0881	-0.0021	-0.0059	0.1175	0.0173	0.1048	4.5177	-16.927	5.6729
9	1.0737	-0.0174	-0.6021	0.5683	0.189	0.8116	0.0033	0.1079	0.0412	-0.0847	0.0182	-0.0539	-0.0382	0.0952	-0.0215	0.0843	0.0052	0.0053	0.1336	0.0222	0.1103	9.5659	-19.4957	2.2931
10	0.8322	0.056	0.0411	0.844	-0.0347	0.9853	0.0059	-0.1345	0.1079	0.1281	-0.0432	0.1869	-0.082	-0.2327	0.0372	0.0952	0.005	0.0263	0.1312	-0.0452	0.098	-19.4324	-14.1429	39.3232
11	0.4615	-0.704	-1.5067	1.5388	1.4355	6.8419	0.0313	0.1831	-0.1336	-0.107	-0.2549	0.3377	-0.1357	-0.8848	0.2236	0.1073	0.0256	-0.0094	0.2809	-0.0784	0.18	-27.3815	-18.4801	23.2667
12	1.6623	0.803	-0.4224	2.3119	0.8076	1.1131	0.0036	0.0225	0.2276	-0.0883	-0.0332	0.2786	-0.2325	-0.2235	0.0296	0.1355	0.0469	-0.0133	0.1468	-0.0172	0.1542	-19.3512	-6.1553	23.512
13	0.4737	0.3938	0.1927	1.8346	0.4965	0.7703	0.028	-0.0364	-0.0007	0.0355	-0.0481	0.0747	0.037	-0.1113	0.02	0.084	0.0051	0.0056	0.0967	0.0083	0.1302	-15.569	-22.1263	17.4962
14	0.4245	0.2172	0.2453	1.363	-0.9959	1.179	0.0068	-0.0633	0.11	0.0461	-0.0572	0.0315	0.0077	0.0149	0.0504	0.1177	0.0158	-0.0034	0.0912	-0.0115	0.1355	-4.1214	-13.2523	28.2356
15	0.5041	0.0016	0.1282	0.465	0.0293	0.8076	0.0005	-0.1462	0.0172	0.1518	-0.066	0.0265	0.003	-0.1254	0.0655	0.1478	-0.0144	0.0291	0.1427	-0.0196	0.1061	-13.8998	-19.3448	40.2365
16	4.1401	-1.3473	0.808	2.2043	-1.6846	5.723	-0.0367	-0.078	0.378	0.1856	-0.018	0.0414	-0.7665	-0.0664	0.0547	0.2945	-0.0072	-0.0301	0.0115	-0.0428	0.2232	-7.8472	6.1049	30.9241
17	0.6865	-0.0254	0.0663	0.5043	0.1317	0.9958	-0.0148	-0.1631	0.0718	0.1498	-0.0371	-0.0016	-0.0464	0.0015	0.0519	0.1698	-0.0128	0.0042	0.13	-0.0275	0.1003	-3.8811	-13.3611	45.7693
18	0.6828	0.1626	-0.2861	1.094	-0.1058	1.2811	0.0307	-0.1925	0.1146	0.192	-0.0528	0.0485	-0.1527	0.0125	0.0221	0.186	-0.015	0.0002	0.133	-0.0564	0.1142	-7.224	-9.7597	49.3117

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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Structure visualization

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 760 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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