PDB-5i9m: Crystal structure of B. pseudomallei FabI in complex with NAD and...

ID or keywords:

Entry

Database: PDB / ID: 5i9m

Title

Crystal structure of B. pseudomallei FabI in complex with NAD and PT408

Components

Enoyl-[acyl-carrier-protein] reductase [NADH]

Keywords

OXIDOREDUCTASE / enoyl-ACP reductase / Burkholderia pseudomallei / diphenyl ethers / slow-binding inhibitors

Function / homology

Function and homology information

enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function

Biological species

Burkholderia pseudomallei (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Hirschbeck, M.W. / Eltschkner, S. / Tonge, P.J. / Kisker, C.

Funding support

Germany, 1items

Citation

Journal: Biochemistry / Year: 2017
Title: Rationalizing the Binding Kinetics for the Inhibition of the Burkholderia pseudomallei FabI1 Enoyl-ACP Reductase.
Authors: Neckles, C. / Eltschkner, S. / Cummings, J.E. / Hirschbeck, M. / Daryaee, F. / Bommineni, G.R. / Zhang, Z. / Spagnuolo, L. / Yu, W. / Davoodi, S. / Slayden, R.A. / Kisker, C. / Tonge, P.J.

History

Deposition	Feb 20, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Feb 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 8, 2017	Group: Database references
Revision 1.2	Apr 19, 2017	Group: Database references
Revision 1.3	Jan 10, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5i9m.cif.gz	307.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5i9m.ent.gz	254 KB	Display	PDB format
PDBx/mmJSON format	5i9m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i9/5i9m ftp://data.pdbj.org/pub/pdb/validation_reports/i9/5i9m	HTTPS FTP

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Related structure data

Related structure data	5i7eC 5i7fC 5i7sC 5i7vC 5i8wC 5i8zC 5i9lC 5i9nC 5iflC 3ek2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5i7f-1 5i9l-1 4m89-1 5ifl-4 5i7f-3 1d8a-1 6ahe-d 5i7f-2 1qsg-1 4zju-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Enoyl-[acyl-carrier-protein] reductase [NADH]

B: Enoyl-[acyl-carrier-protein] reductase [NADH]

C: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

90.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Enoyl-[acyl-carrier-protein] reductase [NADH]

B: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]

B: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

defined by author&software
121 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

C: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

C: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

C: Enoyl-[acyl-carrier-protein] reductase [NADH]

hetero molecules

defined by author&software
121 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.029, 111.217, 260.695
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	C-473- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain 'A' and (resseq 2:258 )
2	1	1	chain 'B' and (resseq 2:258 )
3	1	1	chain 'C' and (resseq 2:258 )

#1: Protein	Enoyl-[acyl-carrier-protein] reductase [NADH] Mass: 29325.391 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) Gene: fabI, fabI_2, ACT79_25590, AM256_11615, AM257_11635, AMS56_08605, DP46_2957, DP49_6839, ERS012314_03793, ERS012372_03823, SY87_14645, TR70_1075, VU09_13745 Production host: Escherichia coli (E. coli) References: UniProt: A0A069B9A4, UniProt: A0A0H3HP34*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-69K / 5-ethyl-4-fluoro-2-[(2-methylpyridin-3-yl)oxy]phenol Mass: 247.265 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₄H₁₄FNO₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.75 Å³/Da / Density % sol: 55.33 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bistris, pH 6.5, 26 % PEG 400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918 Å / Relative weight: 1
Reflection	Resolution: 2.25→47.21 Å / Num. obs: 48130 / % possible obs: 100 % / Redundancy: 6.7 % / R_merge(I) obs: 0.092 / Net I/σ(I): 13
Reflection shell	Resolution: 2.25→2.37 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.619 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.8_1069	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3EK2

3ek2

Resolution: 2.25→47.209 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.64

	R_factor	Num. reflection	% reflection
R_free	0.2808	2441	5.07 %
R_work	0.251	-	-
obs	0.2525	48125	99.99 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.25→47.209 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5736	0	186	303	6225

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6036
X-RAY DIFFRACTION	f_angle_d	1.143	8190
X-RAY DIFFRACTION	f_dihedral_angle_d	13.039	2136
X-RAY DIFFRACTION	f_chiral_restr	0.066	936
X-RAY DIFFRACTION	f_plane_restr	0.004	1038

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1912	X-RAY DIFFRACTION	POSITIONAL
1	2	B	1912	X-RAY DIFFRACTION	POSITIONAL	0.045
1	3	C	1912	X-RAY DIFFRACTION	POSITIONAL	0.053

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2501-2.296	0.4165	144	0.3698	2642	X-RAY DIFFRACTION	100
2.296-2.3459	0.3917	138	0.3664	2648	X-RAY DIFFRACTION	100
2.3459-2.4005	0.3943	147	0.3502	2657	X-RAY DIFFRACTION	100
2.4005-2.4605	0.4147	134	0.3576	2675	X-RAY DIFFRACTION	100
2.4605-2.527	0.3782	132	0.336	2652	X-RAY DIFFRACTION	100
2.527-2.6014	0.3709	152	0.3278	2640	X-RAY DIFFRACTION	100
2.6014-2.6854	0.3812	145	0.3193	2667	X-RAY DIFFRACTION	100
2.6854-2.7813	0.34	156	0.3097	2664	X-RAY DIFFRACTION	100
2.7813-2.8927	0.3298	140	0.3081	2661	X-RAY DIFFRACTION	100
2.8927-3.0243	0.3174	152	0.2907	2673	X-RAY DIFFRACTION	100
3.0243-3.1837	0.3123	155	0.2745	2668	X-RAY DIFFRACTION	100
3.1837-3.3831	0.3211	130	0.2608	2687	X-RAY DIFFRACTION	100
3.3831-3.6443	0.2925	137	0.2524	2713	X-RAY DIFFRACTION	100
3.6443-4.0108	0.2306	147	0.224	2679	X-RAY DIFFRACTION	100
4.0108-4.5908	0.2137	142	0.2003	2728	X-RAY DIFFRACTION	100
4.5908-5.7822	0.1918	153	0.1893	2742	X-RAY DIFFRACTION	100
5.7822-47.2191	0.2081	137	0.1768	2888	X-RAY DIFFRACTION	100

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	6.1325	-1.9916	2.4364	4.7927	-2.3217	5.5096	0.0247	-0.1114	0.7356	0.1446	-0.2783	-0.1472	-0.0756	0.0864	0.2712	0.3028	-0.0325	0.0182	0.152	-0.0269	0.208	4.6445	26.6995	-36.3988
2	1.6423	0.7159	-0.5152	4.8626	-0.7398	0.2202	0.1059	-0.6015	0.535	0.9375	-0.0197	-0.6482	-0.1158	0.2529	-0.1293	0.8586	-0.1404	0.0345	0.5145	-0.1925	0.5123	7.4896	26.6977	-24.9037
3	0.8977	0.017	-0.742	0.3719	0.8011	2.393	0.1066	-0.3828	0.307	0.3726	-0.0906	0.2578	-0.3637	-0.2939	0.1067	0.595	-0.1377	0.1761	0.4161	-0.1867	0.2947	-3.8542	21.7354	-27.4948
4	3.8913	-3.1156	-0.1558	5.6447	-0.2201	2.1387	0.189	-0.3701	0.3623	0.7942	-0.2049	-0.1329	0.0881	0.0295	0.0297	0.4273	-0.1797	0.024	0.2823	-0.048	0.2063	2.3662	6.1639	-29.4957
5	1.3918	0.3036	0.4218	2.3969	0.0529	2.5302	0.0538	-0.0784	0.2889	-0.6032	-0.1966	-0.168	0.0094	0.1494	0.111	0.2875	-0.02	0.0353	0.1278	0.0007	0.1391	3.6752	8.6051	-39.4553
6	0.1123	-0.258	-0.1464	0.5929	0.335	0.189	-0.1043	-0.0267	-0.1506	-0.0159	0.0125	-0.1237	0.1571	0.1146	0.1578	1.1286	0.0743	0.669	0.413	0.0732	0.9801	19.9273	10.1202	-49.4888
7	0.5198	0.5826	-0.0011	1.1387	-0.3493	0.425	-0.0154	0.1959	0.0839	-0.7907	-0.0512	-0.2017	0.1211	0.0842	0.0436	0.8954	0.0651	0.1229	0.19	0.0434	0.2553	4.1733	15.7271	-48.6603
8	0.522	-0.1435	0.2199	0.8834	-0.78	0.9829	0.0619	0.1908	0.1039	-0.2182	0.0744	0.128	-0.1055	-0.1062	-0.052	1.8461	0.1559	-0.0467	0.6964	0.3018	0.7036	-3.0133	26.978	-66.4033
9	0.7466	-0.3032	-0.3726	2.5978	-0.8868	0.6214	0.1078	0.4548	0.1567	-0.5997	-0.0291	0.2592	0.3108	0.0137	-0.146	2.0309	0.1751	-0.0654	1.038	0.5045	0.9617	-5.8766	27.1784	-77.889
10	0.421	0.4228	0.6753	0.5466	0.7236	1.0995	-0.0482	0.2243	0.1027	-0.1585	0.0771	-0.0045	-0.0565	-0.0702	-0.0436	1.8575	0.2891	0.2794	1.1327	0.294	0.6618	6.9661	20.484	-80.325
11	0.6531	-0.0669	-0.2608	0.3719	-0.2742	0.7754	0.3425	0.4299	0.0819	-0.9359	0.0911	0.1884	-0.0554	-0.1381	0.2221	2.3545	0.0384	-0.1136	0.6262	0.2087	0.528	-1.9246	9.631	-70.2484
12	0.52	0.4913	-0.4187	1.6129	-0.4269	0.3437	0.0165	0.4208	-0.0163	-1.3925	0.081	0.409	0.2728	-0.0879	0.0881	1.6476	0.0605	-0.3289	0.3921	0.0522	0.3875	-5.9806	12.2892	-58.4257
13	2.337	0.9355	0.2406	5.988	2.057	4.1789	0.236	-0.1635	-0.0011	0.1668	-0.3924	-0.1914	-0.0457	0.3031	0.1153	0.2147	-0.0521	-0.0062	0.304	0.1143	0.3528	-31.7751	14.6635	-26.3163
14	2.1235	0.6367	1.4856	4.3934	1.516	5.2632	0.0209	-0.0552	-0.0451	-0.4251	-0.0819	-0.0568	0.1866	0.1635	-0.0158	0.236	-0.0346	0.1623	0.311	0.0392	0.5029	-30.1527	15.4005	-27.4714
15	3.6634	3.0581	1.152	6.2234	2.5436	3.6557	0.2038	-0.2632	0.2533	-0.0808	-0.0516	-0.3995	-0.4183	0.5976	-0.1412	0.3945	-0.1351	0.1629	0.5736	0.1857	0.7018	-24.0944	27.1457	-28.2765
16	0.2343	-0.0437	-0.5373	1.887	-0.4338	1.4398	-0.0219	0.1259	0.2997	-0.3935	0.1826	-0.1984	-0.3016	-0.0258	-0.0812	0.2975	-0.0431	0.0128	0.3263	0.0363	0.5315	-32.9373	24.1501	-16.0023
17	1.2422	-0.5713	0.2837	1.4356	-0.4269	2.0999	0.1491	-0.0945	-0.0073	-0.0161	0.0861	0.0951	-0.1205	-0.1314	-0.2412	0.1372	-0.037	0.0474	0.2827	0.0308	0.4962	-35.3112	16.2637	-8.1218
18	2.2999	-0.2415	-0.3415	1.6419	-0.3879	1.5002	-0.1611	-0.1476	0.147	0.0684	0.0875	-0.2053	-0.1341	0.3871	0.1067	0.2006	-0.102	0.0426	0.4278	-0.0462	0.5472	-25.968	12.212	-13.1866
19	1.7705	-0.3297	0.1663	0.8601	-0.6497	1.686	0.0616	0.3109	0.1893	0.1059	0.0388	-0.638	-0.1037	0.5758	-0.0613	0.2562	-0.0527	-0.0136	0.5534	-0.0749	0.8229	-14.9434	1.9913	-10.7604
20	0.7927	-0.1115	0.3719	1.1114	-0.035	1.9794	0.0662	0.2075	0.0924	-0.1692	0.0412	-0.2132	-0.2247	-0.0212	-0.1146	0.155	-0.0471	0.105	0.3513	-0.0131	0.4021	-30.8508	2.8101	-15.8636

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 41 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 42 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 95 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 96 through 139 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 140 through 202 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 203 through 221 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 222 through 258 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 41 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 42 through 67 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 68 through 80 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 81 through 156 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 157 through 258 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 2 through 19 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 20 through 41 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 42 through 55 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 56 through 109 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 110 through 180 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 181 through 202 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 203 through 221 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 222 through 258 )

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