PDB-5onc: Catabolism of the Cholesterol Side Chain in Mycobacterium tubercu...

ID or keywords:

Entry

Database: PDB / ID: 5onc

Title

Catabolism of the Cholesterol Side Chain in Mycobacterium tuberculosis is Controlled by a Redox-Sensitive Thiol Switch

Components

Steroid 3-ketoacyl-CoA thiolase

Keywords

BIOSYNTHETIC PROTEIN / Oxidative Stress / Cholesterol Metabolism / Lipid degradation / Steroid metabolism / Mycobacterium tuberculosis

Function / homology

Function and homology information

acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / phenylacetate catabolic process / cholesterol catabolic process / fatty acid beta-oxidation / identical protein binding
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.19 Å

Authors

Schaefer, C. / Kuper, J. / Sampson, N.S. / Kisker, C.

Funding support

United States,

Germany, 4items

Organization	Grant number	Country
National Institutes of Health	AI092455	United States
National Institutes of Health	RR021008	United States
German Research Foundation	SFB630	Germany
German Research Foundation	FZ82	Germany

Citation

Journal: ACS Infect Dis / Year: 2017
Title: Catabolism of the Cholesterol Side Chain in Mycobacterium tuberculosis Is Controlled by a Redox-Sensitive Thiol Switch.
Authors: Lu, R. / Schaefer, C.M. / Nesbitt, N.M. / Kuper, J. / Kisker, C. / Sampson, N.S.

History

Deposition	Aug 3, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 23, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.2	Jan 17, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5onc.cif.gz	290.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5onc.ent.gz	236.5 KB	Display	PDB format
PDBx/mmJSON format	5onc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5onc_validation.pdf.gz	444.2 KB	Display	wwPDB validaton report
Full document	5onc_full_validation.pdf.gz	457.8 KB	Display
Data in XML	5onc_validation.xml.gz	28.4 KB	Display
Data in CIF	5onc_validation.cif.gz	40.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/on/5onc ftp://data.pdbj.org/pub/pdb/validation_reports/on/5onc	HTTPS FTP

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Related structure data

Related structure data	4ubwS 4ubt 4ubu 4ubv S: Starting model for refinement
Similar structure data	4l61-d 1j9z-2 3rm9-d 4l5z-d 4l6h-d 1ja1-1 3pph-1 5cno-d 2c7z-1 1htr-1 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
Related items in Molecule of the Month	#216 - Dec 2017 Biodegradable Plastic similarity (8) #90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

A: Steroid 3-ketoacyl-CoA thiolase

B: Steroid 3-ketoacyl-CoA thiolase

hetero molecules

84.9 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)	120.289, 120.289, 206.030
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	182
Space group name H-M	P6₃22

Components on special symmetry positions

ID	Model	Components
1	1	A-690- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 1 - 391 / Label seq-ID: 9 - 399

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	Steroid 3-ketoacyl-CoA thiolase / Acetyl-CoA acetyltransferase FadA5 / Beta-ketoacyl-CoA thiolase Mass: 42346.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: fadA5, LH57_19345, Rv3546 / Plasmid: pSD31 / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: I6XHI4, acetyl-CoA C-acyltransferase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.54 Å³/Da / Density % sol: 51.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M citrate, pH 5.5, 0.7 M (NH4)2HPO4, 0.3 M NaCl

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 9, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.19→46.17 Å / Num. obs: 46018 / % possible obs: 100 % / Redundancy: 9.8 % / R_sym value: 0.1 / Net I/σ(I): 15.2
Reflection shell	Resolution: 2.19→2.26 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3897 / CC_1/2: 0.756 / R_sym value: 0.96 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4UBW

4ubw

Resolution: 2.19→46.17 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.942 / SU B: 10.613 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22568	2320	5 %	RANDOM
R_work	0.18213	-	-	-
obs	0.1843	43647	99.91 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 72.984 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.72 Å²	0.36 Å²	0 Å²
2-	-	0.72 Å²	-0 Å²
3-	-	-	-2.33 Å²

Refinement step

Cycle: 1 / Resolution: 2.19→46.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5362	0	5	211	5578

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	5471
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5182
X-RAY DIFFRACTION	r_angle_refined_deg	1.619	1.951	7422
X-RAY DIFFRACTION	r_angle_other_deg	0.866	3	11958
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.534	5	726
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.149	23.82	233
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.958	15	899
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.128	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	861
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6221
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1068
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	3.331	4.129	2903
X-RAY DIFFRACTION	r_mcbond_other	3.328	4.129	2902
X-RAY DIFFRACTION	r_mcangle_it	5.049	6.163	3621
X-RAY DIFFRACTION	r_mcangle_other	5.049	6.164	3622
X-RAY DIFFRACTION	r_scbond_it	3.906	4.444	2567
X-RAY DIFFRACTION	r_scbond_other	3.905	4.445	2568
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.824	6.532	3799
X-RAY DIFFRACTION	r_long_range_B_refined	8.395	49.373	5930
X-RAY DIFFRACTION	r_long_range_B_other	8.379	49.254	5898
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 20646 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.19→2.247 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.344	154	-
R_work	0.31	3152	-
obs	-	-	99.97 %

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	0.7908	-0.3847	0.3411	1.713	-0.9542	2.4094	0.0567	0.0164	-0.0233	0.0502	0.0445	0.1163	0.0527	0.0744	-0.1012	0.0571	-0.0027	0.005	0.0368	-0.0317	0.0525	-57.078	17.677	-16.856
2	7.19	4.1806	-4.7385	2.8104	-1.731	7.0584	-0.653	0.4461	0.6636	-0.6529	0.2786	0.5292	0.3932	0.1724	0.3744	0.6862	0.254	0.0733	0.4573	0.1211	0.2907	-35.892	6.381	-43.354
3	0.3022	-0.4484	-0.5354	3.0834	-0.6749	2.8429	0.0854	-0.0079	-0.0268	-0.0048	-0.2028	-0.1369	0.1488	0.3615	0.1175	0.1745	0.0539	-0.0253	0.1104	-0.0172	0.0408	-48.347	9.429	-11.749
4	1.6673	0.0762	-1.4207	7.6213	-6.0246	5.9612	0.1517	-0.0112	-0.0226	-0.6641	-0.2706	-0.173	0.3765	0.2981	0.119	0.1594	0.0149	0.0311	0.095	-0.0461	0.0596	-53.759	19.003	-33.404
5	1.6961	-0.6676	-0.5937	2.5966	1.5167	3.4327	-0.1018	0.2358	-0.1943	-0.4219	0.043	0.6255	0.4301	0.0443	0.0588	0.3499	-0.0481	-0.1642	0.0857	-0.0062	0.1918	-65.276	-1.887	-32.582
6	0.0272	-0.0928	0.0681	6.5663	-1.8394	0.8516	0.0129	0.0278	-0.051	-0.3054	0.1889	0.2895	-0.0123	-0.0841	-0.2018	0.0821	0.0116	-0.022	0.0952	-0.0188	0.1124	-67.233	23.105	-30.848
7	0.1856	-0.083	0.0044	1.5616	0.1155	2.7008	0.0286	0.0548	-0.0078	-0.1694	-0.0081	0.1687	0.2549	0.0397	-0.0205	0.1179	0.0007	-0.0452	0.0574	-0.0261	0.0471	-58.954	3.477	-24.136
8	0.6579	-0.0159	0.0944	1.4695	-0.5574	2.9612	0.0987	0.0476	-0.0669	-0.2345	0.0503	0.2473	0.5841	0.1438	-0.149	0.2303	0.0141	-0.0692	0.0628	-0.031	0.0744	-60.485	-2.738	-20.379
9	4.5206	1.2014	-0.7291	4.083	-2.0268	3.0313	-0.1158	0.5021	0.0631	-0.9673	-0.4336	-0.9337	0.4208	0.43	0.5494	0.5581	0.2297	0.3673	0.4405	0.059	0.395	-25.446	2.814	-39.532
10	0.9546	-1.5875	-1.6201	3.8317	1.8664	4.2457	0.0719	-0.0089	0.1295	0.1135	-0.173	-0.2018	-0.1255	0.1781	0.101	0.152	-0.0347	0.0042	0.1466	-0.0013	0.1946	-46.321	22.1	-17.471
11	3.5956	1.0432	0.8275	4.939	-1.3554	2.2482	-0.0131	0.5179	-0.4586	-1.1657	-0.0718	-0.464	0.2497	-0.3196	0.0849	0.5109	0.1283	0.1627	0.3185	-0.1162	0.1676	-35.523	-4.987	-35.419
12	3.4751	6.0205	3.5449	12.2436	4.1251	5.8722	0.0317	0.1324	-0.1295	0.1942	0.1736	-0.2007	-0.1482	0.1774	-0.2052	0.0725	0.0356	0.1137	0.0934	0.006	0.2727	-28.004	14.096	-32.405
13	1.6862	-0.7234	-0.9859	5.765	-2.3148	2.287	-0.1667	-0.7163	-0.1104	0.5641	-0.3768	-1.3126	-0.0338	1.1802	0.5435	0.1166	0.1112	-0.2381	1.0351	0.0685	0.8018	-18.193	5.345	-14.157
14	9.7668	6.2225	0.5761	4.3105	-0.2446	1.4469	-0.7479	-0.3186	-0.3619	-0.7764	-0.5575	-0.9425	0.1853	1.0684	1.3054	0.6408	0.0624	0.5205	1.2799	0.7029	1.5561	-14.326	15.638	-36.574
15	2.1542	-0.9241	-1.668	3.705	0.4009	3.3833	-0.1623	-0.338	-0.1475	-0.3583	-0.3267	-0.8744	0.2847	0.8824	0.4889	0.093	0.1453	0.1388	0.4623	0.1394	0.3685	-24.641	1.754	-23.676
16	2.6335	-1.3134	-1.7882	4.3335	1.1679	3.375	-0.4183	-0.5448	-0.2647	0.1692	-0.0648	-1.1321	0.7663	0.7566	0.4831	0.2378	0.3065	0.1281	0.4707	0.2112	0.5403	-24.649	-4.643	-19.866

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 61
2	X-RAY DIFFRACTION	2	A	69 - 92
3	X-RAY DIFFRACTION	3	A	93 - 118
4	X-RAY DIFFRACTION	4	A	119 - 147
5	X-RAY DIFFRACTION	5	A	148 - 191
6	X-RAY DIFFRACTION	6	A	192 - 221
7	X-RAY DIFFRACTION	7	A	222 - 286
8	X-RAY DIFFRACTION	8	A	287 - 391
9	X-RAY DIFFRACTION	9	B	1 - 61
10	X-RAY DIFFRACTION	10	B	69 - 92
11	X-RAY DIFFRACTION	11	B	93 - 118
12	X-RAY DIFFRACTION	12	B	119 - 124
13	X-RAY DIFFRACTION	13	B	149 - 191
14	X-RAY DIFFRACTION	14	B	192 - 221
15	X-RAY DIFFRACTION	15	B	222 - 286
16	X-RAY DIFFRACTION	16	B	287 - 391

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