PDB-3q0g: Crystal Structure of the Mycobacterium tuberculosis Crotonase Bou...

ID or keywords:

Entry

Database: PDB / ID: 3q0g

Title

Crystal Structure of the Mycobacterium tuberculosis Crotonase Bound to a Reaction Intermediate Derived from Crotonyl CoA

Components

enoyl-CoA hydratase echA8

Keywords

LYASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Crotonase / Enoyl CoA Hydratase / PSI-2 / Protein Structure Initiative

Function / homology

Function and homology information

enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid beta-oxidation / peptidoglycan-based cell wall / fatty acid metabolic process / plasma membrane
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.38 Å

Authors

Bruning, J.B. / Delgado, E. / Ghosh, S. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)

Citation

Journal: To be Published
Title: Crystal Structure of the Prokaryotic Crotonase
Authors: Bruning, J.B. / Delgado, E. / Ghosh, S. / Sacchettini, J.C.

History

Deposition	Dec 15, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 11, 2015	Group: Non-polymer description / Other
Revision 1.2	Jan 27, 2016	Group: Non-polymer description
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _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	3q0g.cif.gz	578.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3q0g.ent.gz	479.5 KB	Display	PDB format
PDBx/mmJSON format	3q0g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3q0g_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3q0g_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3q0g_validation.xml.gz	66.5 KB	Display
Data in CIF	3q0g_validation.cif.gz	93 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q0/3q0g ftp://data.pdbj.org/pub/pdb/validation_reports/q0/3q0g	HTTPS FTP

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Related structure data

Related structure data	3pzkC 1mj3S 3q0j C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4fjw-d 3q0j-2 3pzk-d 3h81-d 3q0j-1 4q1j-d 3kqf-2 3moy-1 2vx2-2 3hin-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Other databases	TargetDB: RV1070C

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: enoyl-CoA hydratase echA8

B: enoyl-CoA hydratase echA8

C: enoyl-CoA hydratase echA8

D: enoyl-CoA hydratase echA8

E: enoyl-CoA hydratase echA8

F: enoyl-CoA hydratase echA8

hetero molecules

166 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: enoyl-CoA hydratase echA8

B: enoyl-CoA hydratase echA8

C: enoyl-CoA hydratase echA8

hetero molecules

defined by author&software
82.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: enoyl-CoA hydratase echA8

E: enoyl-CoA hydratase echA8

F: enoyl-CoA hydratase echA8

hetero molecules

defined by author&software
82.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

A: enoyl-CoA hydratase echA8

B: enoyl-CoA hydratase echA8

C: enoyl-CoA hydratase echA8

hetero molecules

A: enoyl-CoA hydratase echA8

B: enoyl-CoA hydratase echA8

C: enoyl-CoA hydratase echA8

hetero molecules

defined by software
166 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: enoyl-CoA hydratase echA8

E: enoyl-CoA hydratase echA8

F: enoyl-CoA hydratase echA8

hetero molecules

D: enoyl-CoA hydratase echA8

E: enoyl-CoA hydratase echA8

F: enoyl-CoA hydratase echA8

hetero molecules

defined by software
166 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	101.640, 133.170, 133.690
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-592- HOH
2	1	C-586- HOH
3	1	E-596- HOH
4	1	E-625- HOH

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	enoyl-CoA hydratase echA8 Mass: 27300.080 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: h37rv / Gene: echA8, MT1100, MTV017.23c, Rv1070c / Plasmid: pVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P64016, UniProt: P9WNN9*PLUS, enoyl-CoA hydratase

#1: Protein

enoyl-CoA hydratase echA8

Mass: 27300.080 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (bacteria) / Strain: h37rv / Gene: echA8, MT1100, MTV017.23c, Rv1070c / Plasmid: pVP16 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P64016, UniProt: P9WNN9*PLUS, enoyl-CoA hydratase

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Non-polymers , 5 types, 856 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#5: Chemical	ChemComp-BCO / Butyryl Coenzyme A / S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} butanethioate (non-preferred name) Mass: 837.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₅H₄₂N₇O₁₇P₃S
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 849 / Source method: isolated from a natural source / Formula: H₂O

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Details

Nonpolymer details	THE COMPOUND PUT DOWN FOR CRYSTALLIZATION IS CROTONYL COA. THE LIGAND (BCO) OBSERVED IN THE ENTRY ...THE COMPOUND PUT DOWN FOR CRYSTALLIZATION IS CROTONYL COA. THE LIGAND (BCO) OBSERVED IN THE ENTRY IS THE REACTION INTERMEDIATE AND THE LIGAND (COA) OBSERVED IN THE ENTRY COULD BE THE HYDROLYSED CROTONYL COA

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.76 Å³/Da / Density % sol: 55.46 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG3350, 0.2 M LiCl, and 20% glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 0.9795 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2009 / Details: mirrors

Radiation

Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.38→20 Å / Num. all: 70756 / Num. obs: 70756 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / R_merge(I) obs: 0.1 / R_sym value: 0.1 / Net I/σ(I): 7.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_sym value	Diffraction-ID	% possible all
2.38-2.44	3.7	0.489	3.41	0.489	1	97.6
2.44-2.49	3.8	0.446	3.89	0.446	1	97.9
2.49-2.53	3.8	0.408	4.33	0.408	1	98.1
2.53-2.58	3.7	0.372	4.89	0.372	1	98.4
2.58-2.64	3.8	0.35	5.2	0.35	1	98.8
2.64-2.7	3.8	0.311	5.73	0.311	1	98.8
2.7-2.77	3.7	0.295	6.33	0.295	1	98.7
2.77-2.84	3.7	0.26	7.5	0.26	1	98.9
2.84-2.93	3.7	0.232	8.28	0.232	1	99
2.93-3.02	3.7	0.198	10.21	0.198	1	98.5
3.02-3.13	3.7	0.17	12.13	0.17	1	98.9
3.13-3.25	3.7	0.142	14.71	0.142	1	98.8
3.25-3.4	3.7	0.118	18.16	0.118	1	99
3.4-3.58	3.7	0.102	22.58	0.102	1	98.7
3.58-3.8	3.9	0.091	26.05	0.091	1	98.6
3.8-4.09	4	0.082	30.42	0.082	1	98.6
4.09-4.5	4.2	0.072	35.31	0.072	1	97.9
4.5-5.14	4.4	0.062	37.53	0.062	1	97.6
5.14-6.44	4.4	0.058	35.44	0.058	1	97.6
6.44-20	4.3	0.041	44.15	0.041	1	95.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHASER		phasing
REFMAC	5.5.0102	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MJ3

1mj3

Resolution: 2.38→19.87 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.909 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.789 / SU ML: 0.204 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.504 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28783	3444	5.1 %	RANDOM
R_work	0.23312	-	-	-
obs	0.23588	64507	93.05 %	-
all	-	67951	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 43.544 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.06 Å²	0 Å²	0 Å²
2-	-	0.15 Å²	0 Å²
3-	-	-	-0.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.38→19.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11126	0	121	849	12096

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.023	11423
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.296	1.977	15469
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.626	5	1525
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.616	23.863	453
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.266	15	1866
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.55	15	91
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	1827
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	8511
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	0.406	1.5	7531
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.749	2	11914
X-RAY DIFFRACTION	r_scbond_it	1.309	3	3892
X-RAY DIFFRACTION	r_scangle_it	2.131	4.5	3547
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.38→2.443 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.335	102	-
R_work	0.241	2062	-
obs	-	-	41.19 %

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	3.4913	-0.484	-0.2629	2.3899	-0.1338	1.4204	-0.0296	-0.4004	0.2753	0.3567	-0.0238	-0.0241	-0.2719	0.1611	0.0535	0.2084	-0.1122	-0.0242	0.1513	-0.0771	0.1394	21.2449	17.6509	-47.9608
2	0.7827	0.2909	-0.0832	0.3091	0.1056	1.1372	-0.0111	-0.0339	0.0407	0.0426	0.0112	-0.0935	-0.1102	0.2673	-0.0001	0.1143	-0.0405	-0.0063	0.163	0.0069	0.1756	20.3774	8.408	-61.8442
3	0.9117	0.4717	0.1331	0.6173	0.3331	1.0423	0.0797	-0.0416	-0.269	0.1266	-0.0247	-0.123	0.2726	0.1735	-0.055	0.1745	0.061	-0.0373	0.0724	0.0261	0.2252	11.3965	-20.7807	-57.106
4	32.4438	5.2168	22.3255	2.055	3.6209	15.3815	0.1196	-0.8364	-0.255	0.7746	0.1492	-0.1301	0.1362	-0.6223	-0.2687	0.4948	0.116	-0.0334	0.5153	0.0497	0.1028	15.121	-4.4101	-30.7324
5	1.0062	0.3737	0.6293	1.1747	-0.2006	1.218	-0.0983	0.3883	-0.0349	-0.2679	0.1423	-0.0259	-0.0786	0.1315	-0.0439	0.1428	-0.0129	0.0755	0.2913	-0.02	0.1011	15.2737	1.4485	-92.0285
6	0.8113	-0.0296	0.0703	0.871	-0.0573	0.5538	0.0188	0.1338	-0.1375	-0.0645	-0.0221	-0.1016	0.1082	0.2213	0.0033	0.1205	0.0318	0.0206	0.1938	-0.0459	0.1481	15.4482	-9.2304	-77.6593
7	2.4382	0.4787	-0.6166	2.4052	1.0188	2.391	0.1421	0.384	0.3032	-0.3431	0.006	0.1089	-0.4233	-0.2985	-0.1481	0.2104	0.1182	-0.0002	0.1481	0.0936	0.1337	27.5388	18.4017	-18.1699
8	0.623	-0.2401	0.0275	0.554	0.0285	1.016	0.0707	0.022	0.03	-0.0666	0.0101	0.1089	-0.1267	-0.2146	-0.0808	0.1168	0.0377	0.0165	0.1631	0.0329	0.1628	31.2791	8.4984	-5.8367
9	1.167	-0.4518	0.0556	0.4358	-0.1611	1.3211	0.1238	0.0335	-0.3026	-0.0932	0.0419	0.1602	0.3226	-0.1818	-0.1657	0.1958	-0.0879	-0.1203	0.0633	0.0106	0.2419	39.1523	-21.8396	-8.8623
10	12.139	3.3866	12.7515	1.8587	3.5	13.4021	0.0597	0.4177	-0.2117	-0.1869	0.1671	-0.0766	0.0618	0.4046	-0.2268	0.2439	0.0466	-0.0082	0.3064	0.034	0.122	38.5083	-2.4549	-31.3282
11	0.8936	0.3472	0.045	1.7572	-0.0855	1.4706	0.0182	-0.2937	-0.027	0.1806	0.0918	0.0721	-0.0688	-0.2783	-0.1099	0.1114	0.0013	0.0371	0.293	0.0438	0.0817	33.997	0.3643	22.1439
12	0.7382	-0.4904	0.0659	0.7766	0.1281	0.736	0.074	-0.176	-0.1615	0.0121	0.0546	0.1294	0.1629	-0.1769	-0.1285	0.1178	-0.0582	-0.045	0.1726	0.076	0.186	36.9182	-11.832	9.6247

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 85
2	X-RAY DIFFRACTION	2	A	86 - 255
3	X-RAY DIFFRACTION	3	B	2 - 231
4	X-RAY DIFFRACTION	4	B	232 - 254
5	X-RAY DIFFRACTION	5	C	1 - 88
6	X-RAY DIFFRACTION	6	C	89 - 255
7	X-RAY DIFFRACTION	7	D	2 - 70
8	X-RAY DIFFRACTION	8	D	76 - 255
9	X-RAY DIFFRACTION	9	E	2 - 224
10	X-RAY DIFFRACTION	10	E	225 - 254
11	X-RAY DIFFRACTION	11	F	3 - 133
12	X-RAY DIFFRACTION	12	F	134 - 254

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Protein , 1 types, 6 molecules ABCDEF

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Non-polymers , 5 types, 856 molecules

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