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- PDB-5lnx: Crystal structure of MmgC, an acyl-CoA dehydrogenase from bacillu... -

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Basic information

Entry
Database: PDB / ID: 5lnx
TitleCrystal structure of MmgC, an acyl-CoA dehydrogenase from bacillus subtilis.
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / DEHYDROGENASE
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / acyl-CoA dehydrogenase activity / sporulation resulting in formation of a cellular spore / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain ...Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsBaker, G.E. / Race, P.R.
CitationJournal: To Be Published
Title: Crystal structure of acyl-CoA dehydrogenase (MmgC) from bacillus subtilis.
Authors: Baker, G.E. / Race, P.R.
History
DepositionAug 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
C: Acyl-CoA dehydrogenase
D: Acyl-CoA dehydrogenase
E: Acyl-CoA dehydrogenase
F: Acyl-CoA dehydrogenase
G: Acyl-CoA dehydrogenase
H: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,24927
Polymers327,9518
Non-polymers7,29719
Water6,215345
1
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
C: Acyl-CoA dehydrogenase
D: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,76215
Polymers163,9764
Non-polymers3,78711
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21750 Å2
ΔGint-135 kcal/mol
Surface area48030 Å2
MethodPISA
2
E: Acyl-CoA dehydrogenase
F: Acyl-CoA dehydrogenase
G: Acyl-CoA dehydrogenase
H: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,48612
Polymers163,9764
Non-polymers3,5118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20250 Å2
ΔGint-143 kcal/mol
Surface area48560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.168, 279.266, 78.191
Angle α, β, γ (deg.)90.00, 101.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A6 - 375
2010B6 - 375
1020A8 - 375
2020C8 - 375
1030A6 - 376
2030D6 - 376
1040A6 - 375
2040E6 - 375
1050A3 - 375
2050F3 - 375
1060A8 - 375
2060G8 - 375
1070A3 - 376
2070H3 - 376
1080B8 - 375
2080C8 - 375
1090B5 - 375
2090D5 - 375
10100B6 - 375
20100E6 - 375
10110B5 - 375
20110F5 - 375
10120B8 - 375
20120G8 - 375
10130B5 - 375
20130H5 - 375
10140C8 - 375
20140D8 - 375
10150C8 - 376
20150E8 - 376
10160C8 - 375
20160F8 - 375
10170C8 - 376
20170G8 - 376
10180C8 - 375
20180H8 - 375
10190D6 - 375
20190E6 - 375
10200D1 - 375
20200F1 - 375
10210D8 - 375
20210G8 - 375
10220D5 - 376
20220H5 - 376
10230E6 - 375
20230F6 - 375
10240E8 - 375
20240G8 - 375
10250E6 - 375
20250H6 - 375
10260F8 - 375
20260G8 - 375
10270F3 - 375
20270H3 - 375
10280G8 - 375
20280H8 - 375

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Acyl-CoA dehydrogenase /


Mass: 40993.910 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: mmgC, yqiN, BSU24150 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P45857, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M MMT pH 8, 25% PEG 1500 and 20 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.481
11L, -K, H20.519
ReflectionResolution: 2.6→48.76 Å / Num. obs: 100379 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 8.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.6→48.76 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.854 / SU B: 9.65 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.077
RfactorNum. reflection% reflectionSelection details
Rfree0.28462 4984 5 %RANDOM
Rwork0.24701 ---
obs0.2489 95343 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.886 Å2
Baniso -1Baniso -2Baniso -3
1--30.1 Å20 Å21.2 Å2
2--47.3 Å20 Å2
3----17.2 Å2
Refinement stepCycle: 1 / Resolution: 2.6→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21390 0 490 345 22225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01922460
X-RAY DIFFRACTIONr_bond_other_d0.0070.0220800
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.98230480
X-RAY DIFFRACTIONr_angle_other_deg1.525347525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.53952963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8224.251861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.329153286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6611592
X-RAY DIFFRACTIONr_chiral_restr0.1050.23417
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0225956
X-RAY DIFFRACTIONr_gen_planes_other0.0070.025040
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3473.55711889
X-RAY DIFFRACTIONr_mcbond_other3.3463.55711889
X-RAY DIFFRACTIONr_mcangle_it5.2255.33114839
X-RAY DIFFRACTIONr_mcangle_other5.2255.33114840
X-RAY DIFFRACTIONr_scbond_it2.8273.55110571
X-RAY DIFFRACTIONr_scbond_other2.8273.55110571
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5035.2815642
X-RAY DIFFRACTIONr_long_range_B_refined7.70728.00926433
X-RAY DIFFRACTIONr_long_range_B_other7.70628.01426425
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A382820.12
12B382820.12
21A371700.11
22C371700.11
31A385620.11
32D385620.11
41A383200.1
42E383200.1
51A372640.1
52F372640.1
61A368660.11
62G368660.11
71A379080.11
72H379080.11
81B364160.11
82C364160.11
91B378520.11
92D378520.11
101B374300.11
102E374300.11
111B366700.1
112F366700.1
121B364860.11
122G364860.11
131B372280.11
132H372280.11
141C364860.11
142D364860.11
151C362520.11
152E362520.11
161C358060.11
162F358060.11
171C362240.1
172G362240.1
181C360100.11
182H360100.11
191D374220.1
192E374220.1
201D368880.1
202F368880.1
211D363000.11
212G363000.11
221D379920.09
222H379920.09
231E361280.1
232F361280.1
241E362160.1
242G362160.1
251E370200.1
252H370200.1
261F356280.1
262G356280.1
271F358320.1
272H358320.1
281G357920.11
282H357920.11
LS refinement shellResolution: 2.599→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 361 -
Rwork0.391 6950 -
obs--98.81 %

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