PDB-3sf6: Crystal structure of Glutaryl-CoA dehydrogenase from Mycobacteriu...

ID or keywords:

Entry

Database: PDB / ID: 3sf6

Title

Crystal structure of Glutaryl-CoA dehydrogenase from Mycobacterium smegmatis

Components

Glutaryl-CoA dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / NIH / NIAID /

SBRI / UW / Emerald BioStructures /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

glutaryl-CoA dehydrogenase (ETF) /

glutaryl-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: 1.7 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	Jun 12, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 29, 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 ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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	3sf6.cif.gz	170.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3sf6.ent.gz	131.5 KB	Display	PDB format
PDBx/mmJSON format	3sf6.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/sf/3sf6 ftp://data.pdbj.org/pub/pdb/validation_reports/sf/3sf6	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 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 4iv6C 4iz9C 4j5iC 4kamC 4lgvC 4o2dC 2ebaS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3swo-d 1siq-1 2dvl-2 3mdd-1 2eba-1 2r0n-2 2jif-d 2vig-1 3mpj-2 1sir-1 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: MysmA.01640.c

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#137 - May 2011 Cytochrome bc1 similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: Glutaryl-CoA dehydrogenase

hetero molecules

44.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glutaryl-CoA dehydrogenase

hetero molecules

A: Glutaryl-CoA dehydrogenase

hetero molecules

A: Glutaryl-CoA dehydrogenase

hetero molecules

A: Glutaryl-CoA dehydrogenase

hetero molecules

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

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	7_545	y+1/2,x-1/2,-z+1/2	1
crystal symmetry operation	10_655	-x+1,-y,z	1
crystal symmetry operation	16_555	-y+1/2,-x+1/2,-z+1/2	1

Unit cell

Length a, b, c (Å)	130.000, 130.000, 101.930
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	98
Space group name H-M	I4₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-565- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	Glutaryl-CoA dehydrogenase / Mass: 43076.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2466 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QV68, glutaryl-CoA dehydrogenase

#1: Protein

Glutaryl-CoA dehydrogenase /

Mass: 43076.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2466 / Plasmid: AVA0421 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QV68,

glutaryl-CoA dehydrogenase

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Non-polymers , 6 types, 348 molecules

#2: Chemical	ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₇H₃₅N₉O₁₅P₂
#3: Chemical	ChemComp-UNL / UNKNOWN LIGAND Num. of mol.: 9 / Source method: obtained synthetically
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.5 Å³/Da / Density % sol: 51 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Internal tracking number 221475C11. JCSG C11. 2 M ammonium sulfate, 0.1 M acetate, pH 4.6, MysmA.01640.c.A1 PS01045 at 45 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.9774

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 28, 2011

Radiation

Monochromator: Asymmetric curved crystal, 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: 1.7→44.573 Å / Num. all: 48013 / Num. obs: 48008 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 16.5 % / B_iso Wilson estimate: 18.942 Å² / R_merge(I) obs: 0.089 / Net I/σ(I): 30.76

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique all	Num. unique obs	% possible all
1.7-1.74		15.85	0.499	6.1	55015	3470	3470	100
1.74-1.79			0.414	7.4	55095		3430	100
1.79-1.84			0.33	9.3	54346		3352	100
1.84-1.9			0.285	11	52758		3213	100
1.9-1.96			0.251	12.6	51947		3152	100
1.96-2.03			0.196	16.1	50419		3017	100
2.03-2.11			0.164	19.4	48984		2932	100
2.11-2.19			0.135	23.2	47894		2836	100
2.19-2.29			0.113	27.7	45582		2715	100
2.29-2.4			0.102	30.5	44018		2598	100
2.4-2.53			0.096	31.9	41837		2470	100
2.53-2.69			0.08	37.3	39883		2366	100
2.69-2.87			0.071	42.2	37141		2203	100
2.87-3.1			0.058	49.9	34945		2079	100
3.1-3.4			0.047	59.9	31771		1904	100
3.4-3.8			0.035	74.6	28497		1738	100
3.8-4.39			0.03	85.6	24830		1549	100
4.39-5.38			0.027	87.6	21868		1322	100
5.38-7.6			0.032	76.4	17004		1045	100
	7.6		0.019	101.3	9297		617	99.2

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	44.57 Å
Translation	2.5 Å	44.57 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER		phasing
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EBA

2eba

Resolution: 1.7→44.573 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.959 / SU B: 2.291 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.072 / 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	0.152	2424	5.1 %	RANDOM
R_work	0.128	-	-	-
obs	0.13	47883	99.73 %	-

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 mean: 11.725 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.27 Å²	0 Å²	0 Å²
2-	-	0.27 Å²	0 Å²
3-	-	-	-0.54 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→44.573 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2895	0	91	330	3316

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.021	3111
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2102
X-RAY DIFFRACTION	r_angle_refined_deg	1.551	1.995	4237
X-RAY DIFFRACTION	r_angle_other_deg	0.966	3	5117
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.193	5	414
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.652	23.077	130
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.159	15	514
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.066	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	474
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3508
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	632
X-RAY DIFFRACTION	r_mcbond_it	0.805	1.5	1945
X-RAY DIFFRACTION	r_mcbond_other	0.25	1.5	819
X-RAY DIFFRACTION	r_mcangle_it	1.411	2	3105
X-RAY DIFFRACTION	r_scbond_it	2.374	3	1166
X-RAY DIFFRACTION	r_scangle_it	3.867	4.5	1118

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.192	180	-
R_work	0.169	3274	-
all	-	3454	-
obs	-	3470	99.65 %

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	0.4659	-0.0475	0.2008	0.4155	-0.0928	0.9822	0.031	0.0124	-0.0595	-0.0675	-0.0205	-0.0625	-0.1139	0.0309	-0.0105	0.0538	-0.0008	0.0115	0.0066	0.0085	0.0309	61.3238	14.626	-1.622
2	2.9399	0.5959	-4.131	1.1677	-0.3552	9.9923	0.3302	0.0317	0.0914	-0.0966	-0.0393	0.1375	-0.7639	-0.1229	-0.2909	0.1029	0.0232	0.009	0.0108	-0.0067	0.0406	45.5977	24.2513	12.0066
3	1.1335	-0.447	-0.6997	3.2983	1.3133	1.9168	-0.006	0.0466	0.0633	-0.0213	0.0521	-0.1111	-0.1748	0.1074	-0.0461	0.0511	0.0016	-0.0158	0.0459	0.0026	0.0182	39.452	15.3318	-0.1004
4	0.5457	0.0781	-0.2184	0.0165	-0.0507	0.1885	-0.0007	0.0374	0.0011	-0.0099	0.0052	0.0037	0.008	-0.0513	-0.0045	0.0491	0.0171	-0.0223	0.0432	-0.0045	0.0331	42.7325	7.3459	0.7783
5	0.4669	-0.0745	0.2012	0.3772	-0.4515	1.6898	0.0066	0.0309	0.0031	-0.058	0.0134	0.0511	0.0444	-0.1388	-0.02	0.0159	0.0066	-0.0178	0.0557	-0.0061	0.0217	30.2922	5.847	2.8168
6	7.8919	0.3478	2.6622	1.1466	0.1439	1.6505	-0.0053	0.0322	-0.4192	-0.0752	0.0728	0.1908	0.1158	-0.1051	-0.0675	0.0398	-0.0334	-0.0211	0.0671	0.0005	0.0923	24.6057	-7.584	12.9234
7	1.1184	-0.0022	-0.1949	0.4362	-0.2388	0.7736	-0.0128	0.0089	-0.0413	-0.0294	0.0009	0.0268	0.0203	-0.1436	0.0119	0.0074	0.0028	-0.0103	0.0511	-0.0084	0.0197	25.9902	1.603	10.7659
8	3.5229	1.3212	0.8497	1.2261	0.5957	0.3171	-0.0346	-0.1508	0.1421	0.0129	-0.0005	0.0463	-0.0073	-0.0373	0.0351	0.0325	0.0205	-0.0077	0.078	-0.0113	0.0296	34.8952	12.05	19.6099
9	3.3354	-1.2159	-1.4381	1.5211	0.914	2.1338	0.0496	0.3069	-0.1927	-0.0557	-0.1514	0.1282	0.0741	-0.3971	0.1018	0.0343	-0.0118	-0.0314	0.0972	-0.0304	0.047	20.3738	-2.805	2.9835
10	4.8059	1.3012	0.2137	1.2177	-0.2881	0.4313	0.0878	0.0825	-0.2203	-0.051	-0.0466	-0.0254	0.0856	0.0362	-0.0412	0.0245	0.0045	-0.0115	0.0293	-0.0101	0.0457	39.5608	-5.5331	5.3193
11	1.3972	1.3993	1.5215	1.6704	1.6015	1.7244	-0.0266	0.018	0.0027	-0.0323	0.0203	-0.0091	-0.0773	-0.0036	0.0063	0.0518	0.014	-0.0023	0.0285	0.0011	0.033	60.3123	15.5627	12.0138
12	2.3712	-0.9224	0.9875	5.7389	-0.6624	7.3363	0.0198	0.1569	0.0466	-0.0228	0.082	-0.2238	-0.6521	0.5549	-0.1019	0.0635	-0.0468	0.0141	0.051	-0.0145	0.0381	76.4696	25.8022	24.8004
13	0.4491	0.2182	0.4259	0.302	0.2888	0.7015	0.0179	0.0093	-0.011	-0.0286	-0.0025	-0.0165	0.0094	0.006	-0.0154	0.0313	0.0009	-0.0035	0.0241	-0.0067	0.0233	64.9286	6.5735	10.0267
14	0.5758	-0.2675	-0.0376	2.1642	0.9671	0.9053	0.0126	-0.0191	-0.0463	-0.0849	-0.087	0.0818	0.019	-0.0526	0.0744	0.0252	0.0035	-0.0035	0.0186	0.0002	0.0271	54.5493	-1.7982	11.2498
15	0.2657	0.0005	0.2726	0.3325	0.2106	0.6466	-0.0326	-0.0241	0.0033	-0.0206	0.0084	-0.0177	-0.1004	-0.041	0.0242	0.0337	0.0047	-0.0068	0.0313	-0.008	0.0279	56.3955	17.6156	21.1617
16	0.7365	-0.3538	-0.1151	2.1702	0.342	0.2785	0.0282	-0.0012	-0.0473	0.0089	-0.0393	0.003	0.0346	-0.0564	0.0111	0.0292	-0.0014	-0.0036	0.0199	-0.0081	0.0263	48.4984	-8.1071	16.0984

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 41
2	X-RAY DIFFRACTION	2	A	42 - 57
3	X-RAY DIFFRACTION	3	A	58 - 78
4	X-RAY DIFFRACTION	4	A	79 - 124
5	X-RAY DIFFRACTION	5	A	125 - 151
6	X-RAY DIFFRACTION	6	A	152 - 168
7	X-RAY DIFFRACTION	7	A	169 - 213
8	X-RAY DIFFRACTION	8	A	214 - 231
9	X-RAY DIFFRACTION	9	A	232 - 243
10	X-RAY DIFFRACTION	10	A	244 - 258
11	X-RAY DIFFRACTION	11	A	259 - 283
12	X-RAY DIFFRACTION	12	A	284 - 289
13	X-RAY DIFFRACTION	13	A	290 - 324
14	X-RAY DIFFRACTION	14	A	325 - 344
15	X-RAY DIFFRACTION	15	A	345 - 372
16	X-RAY DIFFRACTION	16	A	373 - 399

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Protein , 1 types, 1 molecules A

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Non-polymers , 6 types, 348 molecules

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