PDB-4c71: Crystal structure of M. tuberculosis C171Q KasA in complex with TLM18

ID or keywords:

Entry

Database: PDB / ID: 4c71

Title

Crystal structure of M. tuberculosis C171Q KasA in complex with TLM18

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-7RD / FORMIC ACID / : / Chem-M7U / :

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	4c71.cif.gz	347.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4c71.ent.gz	283.5 KB	Display	PDB format
PDBx/mmJSON format	4c71.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4c71_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	4c71_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4c71_validation.xml.gz	41.6 KB	Display
Data in CIF	4c71_validation.cif.gz	62.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c7/4c71 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/4c71	HTTPS FTP

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Related structure data

Related structure data	4c6uC 4c6vC 4c6wC 4c6xC 4c6zC 4c70C 4c72C 4c73C 2wggS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2wgg-1 4c6x-d 2wgf-1 2wgg-4 2wgd-1 2wgg-3 4c73-d 2wgf-4 5w2s-1 5w2o-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

94.3 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)	74.320, 88.870, 184.290
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 , 6 types, 812 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-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Chemical	ChemComp-7RD / (R,E)-3-(4-AZIDOBUTYL)-4-HYDROXY-5-METHYL-5-(2-METHYLBUTA-1,3-DIEN-1-YL)THIOPHEN-2(5H)-ONE Mass: 293.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₁₉N₃O₂S
#6: 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
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 796 / 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: 3.51 Å³/Da / Density % sol: 64.99 % / Description: NONE
Crystal grow	pH: 9.5 / Details: 0.1 M MG-FORMATE, 15% 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 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→33.71 Å / Num. obs: 113762 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 5 % / R_merge(I) obs: 0.11 / Net I/σ(I): 10
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 5 % / R_merge(I) obs: 0.61 / Mean I/σ(I) obs: 2.5 / % 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→92.15 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.958 / SU B: 3.779 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.16796	5684	5 %	RANDOM
R_work	0.13926	-	-	-
obs	0.14073	107829	99.84 %	-

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: 24.148 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.16 Å²	0 Å²	0 Å²
2-	-	1.34 Å²	0 Å²
3-	-	-	-1.18 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→92.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6066	0	175	796	7037

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	6755
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.708	1.976	9219
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.4	5	940
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.179	23.732	284
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.404	15	1056
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.495	15	55
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	1017
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.021	5229
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	1.538	1.5	4310
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.187	2	6926
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.836	3	2445
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.745	4.5	2241
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	0.25	381	-
R_work	0.226	7931	-
obs	-	-	99.9 %

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	0.9686	0.0952	0.0223	0.5872	-0.1261	0.6864	-0.0091	0.0686	-0.1185	-0.0516	-0.027	-0.0836	0.162	0.1281	0.0361	0.0468	0.0375	0.0155	0.0439	0.0159	0.0483	7.2312	-32.9587	10.6717
2	0.7121	0.0268	-0.1754	0.5656	-1.0614	2.1319	-0.0236	-0.0225	-0.2018	-0.0696	-0.1199	-0.0856	0.2607	0.2158	0.1435	0.1836	0.0304	-0.0006	0.0681	0.0423	0.1271	2.8555	-43.5992	26.2868
3	3.0143	1.1391	0.4473	1.9763	0.506	1.3484	0.0244	-0.0844	-0.2002	0.1461	-0.0223	-0.2287	0.1894	0.2434	-0.0021	0.0811	0.0559	-0.0221	0.0926	0.0409	0.0717	13.4138	-33.3908	27.4348
4	1.217	0.5837	0.1962	0.6408	0.0884	0.9064	-0.0008	-0.057	-0.0249	0.0672	0.0048	0.0023	0.1334	0.0171	-0.004	0.0877	0.0144	-0.0069	0.0467	0.0189	0.066	-3.4185	-32.8577	31.7395
5	0.5616	0.0939	0.4028	0.6315	0.1036	1.1633	0.0063	-0.0395	0.0298	0.0415	-0.0315	-0.0849	-0.0071	-0.0136	0.0252	0.0508	0.0113	-0.0084	0.0633	0.0106	0.0845	3.9156	-18.6913	23.7213
6	0.5484	0.0863	-0.0914	0.4866	-0.1503	0.4125	0.0027	0.0653	-0.028	-0.0599	-0.0233	-0.0102	0.1014	0.0166	0.0206	0.0541	0.0228	0.0066	0.0609	0.0051	0.0579	0.9284	-28.2792	9.6365
7	1.9879	-1.1812	2.0798	2.7067	-0.4555	5.5197	0.0034	0.0538	0.1588	0.0773	-0.0046	-0.3267	-0.0117	0.5916	0.0012	0.0086	-0.0302	-0.0165	0.2078	0.036	0.1638	23.9436	-18.7368	22.8447
8	0.6543	-0.1134	-0.1301	0.5534	0.0557	0.6167	0.0172	0.0954	0.0808	-0.061	-0.0563	-0.0535	-0.0203	0.0922	0.0391	0.053	0.0112	0.0048	0.0827	0.0294	0.0677	5.2301	-16.4204	6.1766
9	1.006	-0.0126	-0.2586	0.5845	0.0687	1.3618	0.0171	0.069	0.0321	-0.0846	-0.0269	-0.0615	-0.0205	0.1801	0.0099	0.038	0.0135	0.02	0.0777	0.0385	0.0637	10.364	-18.937	2.4925
10	0.9993	0.3998	0.0646	1.0447	0.0561	0.8367	-0.0015	-0.1211	0.0678	0.0834	-0.0517	0.1275	-0.043	-0.2393	0.0532	0.0254	0.0065	0.0207	0.0892	-0.0332	0.0364	-19.1582	-14.4276	39.0826
11	0.5958	0.381	-0.5674	1.3872	1.6296	4.071	-0.0232	0.0838	0.129	-0.1364	-0.1578	0.2575	-0.1999	-0.5354	0.181	0.0542	0.0344	-0.0107	0.1766	-0.0248	0.1001	-26.491	-19.2996	22.502
12	1.371	1.0936	0.1286	4.0134	0.0017	1.2573	-0.0018	0.0207	0.1941	-0.0684	-0.0288	0.2713	-0.194	-0.2061	0.0306	0.0583	0.0597	-0.0047	0.0901	-0.0125	0.0933	-19.096	-6.3727	23.32
13	0.1966	0.2854	0.0145	1.5347	0.3056	0.6339	0.0165	-0.0115	0.016	0.0054	-0.0314	0.0609	0.0223	-0.0777	0.0149	0.0482	0.0078	-0.0056	0.0655	0.0112	0.0868	-14.813	-22.3001	17.3752
14	0.5011	0.7224	-0.2054	1.6386	-0.9391	0.941	0.0372	-0.0549	0.0644	0.0199	-0.0549	0.0345	0.0684	0.0007	0.0177	0.0629	0.0169	-0.007	0.0538	-0.0063	0.0775	-3.852	-13.3467	28.4387
15	0.6259	0.0421	0.1195	0.3759	0.1691	0.5377	0.0048	-0.1435	0.0148	0.1084	-0.0424	0.0553	0.0207	-0.1269	0.0375	0.074	-0.0124	0.0257	0.074	-0.0184	0.0455	-13.7158	-19.8295	40.3015
16	3.3805	-0.3573	1.2878	1.7203	-0.7627	4.0412	-0.0306	0.0541	0.3408	0.0084	-0.0454	0.0629	-0.4448	0.0211	0.076	0.1914	0.0254	-0.0181	0.0179	-0.0382	0.168	-8.0323	5.948	31.236
17	0.5533	-0.0307	-0.1461	0.4547	0.0306	0.9004	-0.0004	-0.1425	0.0524	0.1494	-0.0372	-0.0085	-0.0298	-0.0198	0.0377	0.0999	-0.0085	-0.004	0.0695	-0.0281	0.0413	-3.8885	-13.5677	46.0019
18	0.836	0.0289	-0.1473	1.1427	-0.0435	1.1415	0.0406	-0.2004	0.0961	0.1691	-0.0437	0.0555	-0.1087	-0.0664	0.003	0.106	-0.0058	-0.004	0.0824	-0.0532	0.0462	-7.5083	-9.9092	49.4714

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 , 6 types, 812 molecules

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