PDB-3q1t: Crystal structure of enoyl-coA hydratase from Mycobacterium avium

ID or keywords:

Entry

Database: PDB / ID: 3q1t

Title

Crystal structure of enoyl-coA hydratase from Mycobacterium avium

Components

Enoyl-CoA hydratase

Keywords

LYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / enoyl-CoA / hydratase / non-pathogenic species / mycobacterium / tuberculosis / fatty acid metabolism / acetyl CoA

Function / homology

Function and homology information

enoyl-CoA hydratase activity / fatty acid metabolic process
Similarity search - Function

Biological species

Mycobacterium avium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.35 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...

History

Deposition	Dec 17, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 19, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Apr 22, 2015	Group: Database references
Revision 1.3	Sep 13, 2023	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 / struct_ref_seq_dif 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 / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3q1t.cif.gz	562.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3q1t.ent.gz	466.3 KB	Display	PDB format
PDBx/mmJSON format	3q1t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3q1t_validation.pdf.gz	478.2 KB	Display	wwPDB validaton report
Full document	3q1t_full_validation.pdf.gz	489.1 KB	Display
Data in XML	3q1t_validation.xml.gz	53.8 KB	Display
Data in CIF	3q1t_validation.cif.gz	75.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q1/3q1t ftp://data.pdbj.org/pub/pdb/validation_reports/q1/3q1t	HTTPS FTP

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Related structure data

Related structure data	3gvcC 3gvgC 3gwcC 3h7fC 3h81C 3he2C 3hwiC 3hwkC 3hzgC 3icoC 3khpC 3llsC 3moyC 3mpzC 3mybC 3ndnC 3ndoC 3nf4C 3ng3C 3njdC 3nwoC 3o0mC 3o38C 3oc6C 3oc7C 3oi9C 3oksC 3omeC 3p0tC 3p2yC 3p4iC 3p4tC 3p5mC 3p85C 3pe8C 3pk0C 3ppiC 3pzyC 3q8nC 3qbpC 3qdfC 3qhaC 3qivC 3qk8C 3qkaC 3qljC 3qmjC 3qreC 3quaC 3quvC 3qxiC 3qxzC 3qyrC 3r0oC 3r1iC 3r1jC 3r20C 3r2nC 3r4tC 3r6hC 3r6oC 3r7kC 3r8cC 3r9pC 3r9qC 3r9rC 3r9sC 3r9tC 3rd5C 3rd7C 3rd8C 3rfqC 3rihC 3rr2C 3rr6C 3rrpC 3rrvC 3rsiC 3rv2C 3s82C 3sbxC 3sf6C 3sllC 3svkC 3svtC 3swoC 3swtC 3swxC 3t3wC 3tavC 3tcrC 3tdeC 3tjrC 3tl3C 3tlfC 3trrC 3tx2C 3tzqC 3tzuC 3u0aC 3ucxC 3uveC 4di1C 4dieC 4dq8C 4dxlC 4ed4C 4egeC 4egfC 4emdC 4eo9C 4eyeC 4f3wC 4f47C 4ffcC 4gk6C 4hdtC 4hr3C 4i1yC 4ijnC 4iv6C 4iz9C 4j5iC 4kamC 4lgvC 4o2dC 1wz8S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3qk8-d 2iex-2 7m3w-1 1wz8-d 6ojm-3 3sll-d 5k4g-1 2uzf-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
Other databases	TargetDB: MyavA.00829.e

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Enoyl-CoA hydratase

B: Enoyl-CoA hydratase

C: Enoyl-CoA hydratase

D: Enoyl-CoA hydratase

E: Enoyl-CoA hydratase

F: Enoyl-CoA hydratase

178 kDa, 6 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)	124.920, 136.890, 104.380
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 5 / Auth seq-ID: 11 - 255 / Label seq-ID: 15 - 259

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F

#1: Protein	Enoyl-CoA hydratase Mass: 29584.727 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_3574 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QIL3, UniProt: A0A0H2ZRU2*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.51 Å³/Da / Density % sol: 51.07 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: MyavA00829eA1 3C protease cleaved PW28936 at 23.9 mg/mL against JCSG+ screen condition H3, 0.1 M BisTris pH 5.5, 25% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID ...Details: MyavA00829eA1 3C protease cleaved PW28936 at 23.9 mg/mL against JCSG+ screen condition H3, 0.1 M BisTris pH 5.5, 25% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 216914h3., VAPOR DIFFUSION, SITTING DROP

Crystal

Density Matthews: 2.51 Å³/Da / Density % sol: 51.07 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MyavA00829eA1 3C protease cleaved PW28936 at 23.9 mg/mL against JCSG+ screen condition H3, 0.1 M BisTris pH 5.5, 25% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.97946 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97946 Å / Relative weight: 1

Reflection

Number: 360202 / R_merge(I) obs: 0.068 / D res high: 2.35 Å / Num. obs: 74741 / % possible obs: 99.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs
10.51	50	917	96.1	1	0.018
7.43	10.51	1618	99.1	1	0.021
6.07	7.43	2048	99.1	1	0.029
5.25	6.07	2393	99.2	1	0.035
4.7	5.25	2708	99.4	1	0.034
4.29	4.7	2967	99.7	1	0.034
3.97	4.29	3236	99.7	1	0.036
3.72	3.97	3359	97.4	1	0.049
3.5	3.72	3595	97.3	1	0.055
3.32	3.5	3843	99.1	1	0.069
3.17	3.32	4049	99.7	1	0.089
3.03	3.17	4252	99.9	1	0.113
2.91	3.03	4409	99.9	1	0.132
2.81	2.91	4606	99.8	1	0.165
2.71	2.81	4727	99.9	1	0.202
2.63	2.71	4905	99.4	1	0.292
2.55	2.63	5044	99.9	1	0.291
2.48	2.55	5216	99.8	1	0.339
2.41	2.48	5349	99.9	1	0.405
2.35	2.41	5500	99.9	1	0.52

Reflection

Resolution: 2.35→50 Å / Num. all: 75179 / Num. obs: 74741 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / R_merge(I) obs: 0.068 / Net I/σ(I): 16.58

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Diffraction-ID	% possible all
2.35-2.41	0.52	2.82	5505	1	99.9
7.43-10.51	0.021	48.55	1632	1	99.1
6.07-7.43	0.029	39.57	2066	1	99.1
5.25-6.07	0.035	36.7	2412	1	99.2
4.7-5.25	0.034	37.88	2725	1	99.4
4.29-4.7	0.034	37.84	2975	1	99.7
3.97-4.29	0.036	36.03	3246	1	99.7
3.72-3.97	0.049	28.44	3448	1	97.4
3.5-3.72	0.055	25.82	3694	1	97.4
3.32-3.5	0.069	20.34	3878	1	99.1
3.17-3.32	0.089	15.92	4063	1	99.7
3.03-3.17	0.113	12.49	4258	1	99.9
2.91-3.03	0.132	10.58	4413	1	99.9
2.81-2.91	0.165	8.77	4616	1	99.8
2.71-2.81	0.202	7.2	4732	1	99.9
2.63-2.71	0.292	5.49	4933	1	99.4
2.55-2.63	0.291	5.02	5049	1	99.9
2.48-2.55	0.339	4.34	5228	1	99.8
2.41-2.48	0.405	3.59	5352	1	99.9
10.51-50	0.018	49.58	954	1	96.1

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 52.61 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3 Å	48.77 Å
Translation	3 Å	48.77 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.1.4	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1wz8

1wz8

Resolution: 2.35→50 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.93 / WR_factor R_free: 0.214 / WR_factor R_work: 0.1761 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8543 / SU B: 14.376 / SU ML: 0.154 / SU R Cruickshank DPI: 0.3162 / SU R_free: 0.2215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2273	3771	5.1 %	RANDOM
R_work	0.1891	-	-	-
obs	0.191	74523	99.15 %	-

Solvent computation

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

Displacement parameters

B_iso max: 81.88 Å² / B_iso mean: 38.4215 Å² / B_iso min: 9.8 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.12 Å²	0 Å²	0 Å²
2-	-	0.69 Å²	0 Å²
3-	-	-	-0.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11311	0	0	348	11659

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.021	11542
X-RAY DIFFRACTION	r_angle_refined_deg	1.409	1.963	15711
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.613	5	1531
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.057	23.761	468
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.464	15	1785
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.972	15	81
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	1826
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	8755
X-RAY DIFFRACTION	r_mcbond_it	0.57	1.5	7564
X-RAY DIFFRACTION	r_mcangle_it	1.087	2	12025
X-RAY DIFFRACTION	r_scbond_it	2.002	3	3978
X-RAY DIFFRACTION	r_scangle_it	3.277	4.5	3683

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	978	MEDIUM POSITIONAL	0.12	0.5
2	B	978	MEDIUM POSITIONAL	0.14	0.5
3	C	978	MEDIUM POSITIONAL	0.14	0.5
4	D	978	MEDIUM POSITIONAL	0.13	0.5
5	E	978	MEDIUM POSITIONAL	0.15	0.5
6	F	978	MEDIUM POSITIONAL	0.15	0.5
1	A	803	LOOSE POSITIONAL	0.36	5
2	B	803	LOOSE POSITIONAL	0.36	5
3	C	803	LOOSE POSITIONAL	0.4	5
4	D	803	LOOSE POSITIONAL	0.31	5
5	E	803	LOOSE POSITIONAL	0.32	5
6	F	803	LOOSE POSITIONAL	0.34	5
1	A	978	MEDIUM THERMAL	0.52	2
2	B	978	MEDIUM THERMAL	0.61	2
3	C	978	MEDIUM THERMAL	0.59	2
4	D	978	MEDIUM THERMAL	0.65	2
5	E	978	MEDIUM THERMAL	0.59	2
6	F	978	MEDIUM THERMAL	0.6	2
1	A	803	LOOSE THERMAL	0.79	10
2	B	803	LOOSE THERMAL	0.84	10
3	C	803	LOOSE THERMAL	0.76	10
4	D	803	LOOSE THERMAL	0.84	10
5	E	803	LOOSE THERMAL	0.76	10
6	F	803	LOOSE THERMAL	0.75	10

LS refinement shell

Resolution: 2.35→2.411 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.31	270	-
R_work	0.259	5205	-
all	-	5475	-
obs	-	-	99.73 %

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	1.1473	-0.0434	-0.3967	0.3538	-0.1543	0.6856	-0.0838	0.261	-0.0732	-0.0672	-0.0432	-0.0503	0.1354	0.0425	0.1269	0.1215	0.0107	0.0698	0.1741	-0.0143	0.0516	100.1567	20.4269	62.3672
2	0.678	0.193	0.1498	0.7832	0.1305	0.5391	-0.0522	-0.0015	0.0932	0.0538	-0.0035	0.0163	-0.0926	-0.0777	0.0557	0.1109	0.0211	-0.0296	0.0463	-0.0173	0.0383	79.6157	51.4528	94.2702
3	0.6346	-0.0429	-0.1447	0.5019	-0.1359	0.3972	-0.0516	-0.0159	0.0122	0.0166	-0.0265	-0.0988	-0.0237	0.1027	0.0781	0.0526	-0.0143	-0.0457	0.1062	0.0244	0.077	108.8287	34.7549	91.4033
4	0.6565	-0.4198	-0.2142	0.7498	0.0954	0.3793	-0.1093	-0.0281	-0.1194	0.0899	-0.0024	0.0684	0.1146	-0.0344	0.1118	0.1202	-0.0145	0.0515	0.0498	0.0226	0.0614	80.2883	16.7976	96.3964
5	1.1114	0.0254	-0.0962	0.5819	0.0879	0.5787	-0.0386	0.25	0.1729	-0.1636	-0.0489	-0.0654	-0.1445	-0.0181	0.0875	0.1733	-0.0097	-0.0204	0.1568	0.0891	0.0755	87.4459	52.2626	62.5803
6	0.6995	-0.5284	0.0788	1.3155	-0.1189	0.5418	-0.0482	0.1856	-0.1615	-0.1611	-0.0746	0.1974	0.0806	-0.1693	0.1228	0.0998	-0.0591	-0.0096	0.2108	-0.08	0.0975	66.4597	26.1027	66.5881

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-10 - 9999
2	X-RAY DIFFRACTION	2	B	-10 - 9999
3	X-RAY DIFFRACTION	3	C	-10 - 9999
4	X-RAY DIFFRACTION	4	D	-10 - 9999
5	X-RAY DIFFRACTION	5	E	-10 - 9999
6	X-RAY DIFFRACTION	6	F	-10 - 9999

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