PDB-4iv6: X-ray crystal structure of an isovaleryl-CoA dehydrogenase from M...

ID or keywords:

Entry

Database: PDB / ID: 4iv6

Title

X-ray crystal structure of an isovaleryl-CoA dehydrogenase from Mycobacterium smegmatis

Components

Acyl-CoA dehydrogenase FadE3

Keywords

OXIDOREDUCTASE /

Structural Genomics / NIAID /

National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

acyl-CoA dehydrogenase activity /

flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 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	Jan 22, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 20, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 22, 2015	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	4iv6.cif.gz	313.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4iv6.ent.gz	255.5 KB	Display	PDB format
PDBx/mmJSON format	4iv6.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/iv/4iv6 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/4iv6	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 3q1tC 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 3u0bC 3ucxC 3uveC 4di1C 4dieC 4dq8C 4dxlC 4ed4C 4egeC 4egfC 4emdC 4eo9C 4eyeC 4f3wC 4f47C 4ffcC 4gk6C 4hdtC 4hr3C 4i1yC 4ijnC 4iz9C 4j5iC 4kamC 4lgvC 4o2dC C: citing same article (ref.)
Similar structure data	5lnx-2 1ws9-1 3pfd-d 3mpi-2 4m9a-d 5lnx-1 4p13-d 3mdd-1 2vig-2 1ivh-d 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	TargetTrack: SSGCID-MysmA.01263.c

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Acyl-CoA dehydrogenase FadE3

B: Acyl-CoA dehydrogenase FadE3

hetero molecules

86.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Acyl-CoA dehydrogenase FadE3

B: Acyl-CoA dehydrogenase FadE3

hetero molecules

A: Acyl-CoA dehydrogenase FadE3

B: Acyl-CoA dehydrogenase FadE3

hetero molecules

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

Unit cell

Length a, b, c (Å)	105.820, 105.820, 169.490
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-582- HOH
2	1	B-745- HOH

#1: Protein	Acyl-CoA dehydrogenase FadE3 / Isovaleryl-CoA dehydrogenase Mass: 42329.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: fadE3, MSMEI_1947 / Production host: Escherichia coli (E. coli) References: UniProt: A0QTW7, short-chain acyl-CoA dehydrogenase
#2: Chemical	ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₅N₉O₁₅P₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 665 / 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: 2.8 Å³/Da / Density % sol: 56.11 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: JCSG+ well B10: 0.2 M magnesium chloride, 0.1 M sodium cacodylate, pH 6.50, 50% PEG200, 21.63 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.9774 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2012

Radiation

Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9774 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. all: 65695 / Num. obs: 64445 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 26.487 Å² / R_merge(I) obs: 0.104 / Net I/σ(I): 13.73

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2-2.05		0.551	3.31	27743	4720	99.4
2.05-2.11		0.451	4.04	27292	4651	99.4
2.11-2.17		0.377	4.85	26404	4496	99.2
2.17-2.24		0.311	5.86	25684	4365	99.2
2.24-2.31		0.27	6.75	24890	4246	99.1
2.31-2.39		0.23	7.71	24087	4087	98.8
2.39-2.48		0.196	9.06	23331	3953	98.8
2.48-2.58		0.172	10.04	22637	3832	98.7
2.58-2.7		0.146	11.76	21459	3636	98.4
2.7-2.83		0.125	13.3	20655	3499	98.3
2.83-2.98		0.104	15.37	19599	3326	98.1
2.98-3.16		0.087	18.16	18462	3149	97.9
3.16-3.38		0.072	21.64	17325	2964	97.6
3.38-3.65		0.06	25.38	15984	2758	97.2
3.65-4		0.05	29.6	14589	2528	96.8
4-4.47		0.046	31.49	13243	2304	96.4
4.47-5.16		0.044	31.23	11558	2043	96
5.16-6.32		0.046	29.04	10085	1743	95.1
6.32-8.94		0.035	33.07	7922	1356	93.6
	8.94	0.028	38.25	4357	789	89.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
REFMAC	5.7.0032	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→45.62 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.152 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.125 / 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	0.1848	3267	5.1 %	RANDOM
R_work	0.1495	-	-	-
obs	0.1513	64429	98.21 %	-
all	-	65695	-	-

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 max: 57.76 Å² / B_iso mean: 22.593 Å² / B_iso min: 5.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.21 Å²	-0 Å²	-0 Å²
2-	-	-0.21 Å²	0 Å²
3-	-	-	0.42 Å²

Refinement step

Cycle: LAST / Resolution: 2→45.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5809	0	106	665	6580

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	6134
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5881
X-RAY DIFFRACTION	r_angle_refined_deg	1.441	1.997	8330
X-RAY DIFFRACTION	r_angle_other_deg	0.815	3	13537
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.62	5	799
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.133	23.793	261
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.37	15	1063
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.82	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	926
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6972
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1349
X-RAY DIFFRACTION	r_mcbond_it	0.74	1.17	3094
X-RAY DIFFRACTION	r_mcbond_other	0.738	1.17	3093
X-RAY DIFFRACTION	r_mcangle_it	1.202	1.751	3873

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.268	255	-
R_work	0.206	4465	-
all	-	4720	-
obs	-	-	99.45 %

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	2.4416	1.0601	-2.4326	5.4486	-3.0553	8.3318	-0.0969	0.0458	-0.3792	-0.2176	-0.0838	0.1464	1.0736	0.3298	0.1807	0.1872	0.0543	-0.0327	0.0503	-0.045	0.1728	53.7102	10.0094	28.2852
2	6.2539	0.0907	-3.621	0.8073	-0.3516	3.5541	-0.0032	0.1327	-0.2951	-0.1035	0.1196	0.2272	0.2802	-0.0815	-0.1164	0.1019	-0.0544	-0.078	0.0967	-0.0021	0.1591	42.2419	14.4066	25.0052
3	0.7391	-0.0594	-0.0281	0.3563	-0.0394	0.6245	0.0233	0.1208	-0.1496	-0.0555	0.0215	0.1537	0.0928	-0.1599	-0.0448	0.0347	-0.0326	-0.0416	0.1172	0.0044	0.0974	40.8639	24.4304	30.0499
4	1.3027	-1.0864	-0.4076	2.1202	0.4576	1.8953	0.0669	0.2462	-0.0693	-0.107	-0.0096	0.2242	-0.1002	-0.2975	-0.0573	0.0474	0.0184	-0.0555	0.1964	0.0472	0.1011	35.0103	38.2317	23.0119
5	0.4634	-0.1277	-0.1955	0.3386	-0.0896	0.2427	0.0124	0.0447	-0.1152	-0.0521	0.0189	0.1015	0.0565	-0.0646	-0.0313	0.0673	-0.0064	-0.023	0.0881	0.0023	0.0732	55.1471	24.6017	33.8301
6	1.6813	-0.5179	-1.1262	0.3843	0.5106	1.3068	-0.011	0.0376	-0.0834	-0.0248	0.0122	0.0399	0.0416	-0.0453	-0.0013	0.0829	0.0041	-0.0019	0.0514	0.0029	0.0633	63.3682	25.178	32.9602
7	1.0475	-0.344	-1.4289	0.4332	0.6322	4.2776	0.0196	-0.0365	-0.1077	-0.0263	0.0087	0.1036	0.0106	-0.0462	-0.0282	0.057	0.0059	-0.0094	0.0865	0.0312	0.0872	52.0485	35.8062	43.3216
8	3.3171	2.882	0.7813	5.2078	0.2926	2.2125	-0.1336	0.1587	0.3174	-0.1276	-0.0004	0.2143	-0.5088	-0.1722	0.134	0.1842	0.0745	0.0186	0.0653	0.0331	0.064	77.5092	48.5085	12.5074
9	0.9244	-0.2306	-0.3106	0.9488	0.3108	0.3691	0.0202	0.1039	0.0352	-0.1089	0.0073	-0.176	-0.1267	-0.0426	-0.0275	0.1237	-0.0057	0.0508	0.0526	0.0084	0.075	90.3359	39.5892	11.0289
10	1.667	-0.2037	-1.0907	0.9456	0.0929	2.2871	-0.0398	-0.0302	-0.0457	-0.0202	-0.0194	-0.0813	0.0131	0.0949	0.0592	0.0634	0.0017	0.0452	0.0563	-0.0086	0.0562	94.7648	16.4333	16.1566
11	1.3647	-0.5727	0.4552	1.9161	-0.1103	1.7187	-0.0521	0.0061	0.0244	-0.0071	0.0292	-0.1663	-0.0303	0.0395	0.0229	0.0571	-0.0045	0.0469	0.0277	-0.0117	0.0546	95.1677	20.7802	13.4027
12	1.7657	-0.4798	-0.6649	0.7767	0.6129	1.0737	-0.0284	0.1462	0.0433	-0.0739	0.0071	-0.1191	-0.0299	0.0123	0.0213	0.0652	-0.0139	0.0297	0.0212	0.006	0.053	92.5742	22.6557	13.0616
13	2.4544	-0.4529	-0.5491	0.2456	0.0548	0.3663	0.045	0.0237	0.0169	-0.0578	-0.0141	-0.0038	-0.0367	-0.0082	-0.031	0.0896	0.0096	0.0187	0.0437	0.0045	0.0479	74.3024	45.6517	29.4452
14	1.3926	-0.3096	0.4642	0.3081	-0.129	0.5984	0.0278	0.0861	0.0316	-0.0485	-0.0291	-0.0265	-0.001	0.0373	0.0013	0.0835	0.0105	0.0094	0.0551	0.009	0.0507	78.5612	35.9081	30.1505

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 31
2	X-RAY DIFFRACTION	2	A	32 - 61
3	X-RAY DIFFRACTION	3	A	62 - 134
4	X-RAY DIFFRACTION	4	A	135 - 196
5	X-RAY DIFFRACTION	5	A	197 - 307
6	X-RAY DIFFRACTION	6	A	308 - 356
7	X-RAY DIFFRACTION	7	A	357 - 384
8	X-RAY DIFFRACTION	8	B	2 - 31
9	X-RAY DIFFRACTION	9	B	32 - 120
10	X-RAY DIFFRACTION	10	B	121 - 154
11	X-RAY DIFFRACTION	11	B	155 - 195
12	X-RAY DIFFRACTION	12	B	196 - 233
13	X-RAY DIFFRACTION	13	B	234 - 307
14	X-RAY DIFFRACTION	14	B	308 - 384

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