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- PDB-8ciw: Methylsuccinyl-CoA dehydrogenase from Pseudomonas migulae with bo... -

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Basic information

Entry
Database: PDB / ID: 8ciw
TitleMethylsuccinyl-CoA dehydrogenase from Pseudomonas migulae with bound FAD and (2S)-methylsuccinyl-CoA
Components(2S)-methylsuccinyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / FAD / dehydrogenase / methylsuccinyl-CoA
Function / homology
Function and homology information


acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 ...Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / CITRATE ANION / (2S)-Methylsuccinyl-CoA / (2S)-methylsuccinyl-CoA dehydrogenase
Similarity search - Component
Biological speciesPseudomonas migulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZarzycki, J. / McLean, R. / Erb, T.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Sci Adv / Year: 2023
Title: Exploring alternative pathways for the in vitro establishment of the HOPAC cycle for synthetic CO 2 fixation.
Authors: McLean, R. / Schwander, T. / Diehl, C. / Cortina, N.S. / Paczia, N. / Zarzycki, J. / Erb, T.J.
History
DepositionFeb 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (2S)-methylsuccinyl-CoA dehydrogenase
B: (2S)-methylsuccinyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,25610
Polymers119,4012
Non-polymers4,8568
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-20 kcal/mol
Surface area38180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.805, 169.563, 118.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-882-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein (2S)-methylsuccinyl-CoA dehydrogenase


Mass: 59700.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas migulae (bacteria) / Gene: SAMN04490194_2123 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1H5ILA2

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Non-polymers , 6 types, 575 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-ZKK / (2S)-Methylsuccinyl-CoA / (3S)-4-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-3-methyl-4-oxidanylidene-butanoic acid


Mass: 881.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H42N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Enzyme (20 mg/mL) in 25 mM MOPS pH 7.5 and 0.2 M NaCl was mixed in a 1:1 ratio with crystallization condition (0.2 M ammonium citrate pH 5.0, 20% (w/v) PEG 3350). Soaking and cryoprotection ...Details: Enzyme (20 mg/mL) in 25 mM MOPS pH 7.5 and 0.2 M NaCl was mixed in a 1:1 ratio with crystallization condition (0.2 M ammonium citrate pH 5.0, 20% (w/v) PEG 3350). Soaking and cryoprotection of crystals was performed by adding methylsuccinyl-CoA and PEG200 to final concentrations of 16 mM and 40% (v/v), respectively, before crystals were plunge frozen in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.93→25.01 Å / Num. obs: 105292 / % possible obs: 99.7 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rpim(I) all: 0.034 / Rrim(I) all: 0.124 / Net I/σ(I): 14.6 / Num. measured all: 1387714
Reflection shellResolution: 1.93→2.03 Å / % possible obs: 98.6 % / Redundancy: 12.7 % / Num. measured all: 191262 / Num. unique obs: 15053 / CC1/2: 0.892 / Rpim(I) all: 0.337 / Rrim(I) all: 1.213 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.20.1refinement
XDS20190315data reduction
PHENIX1.20.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→25.01 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.97 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2027 1997 1.9 %
Rwork0.1739 --
obs0.1744 105172 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→25.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8632 0 26 567 9225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098805
X-RAY DIFFRACTIONf_angle_d0.96711943
X-RAY DIFFRACTIONf_dihedral_angle_d15.6433182
X-RAY DIFFRACTIONf_chiral_restr0.0521356
X-RAY DIFFRACTIONf_plane_restr0.0091518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.31331370.28457083X-RAY DIFFRACTION97
1.98-2.030.26491410.2477320X-RAY DIFFRACTION100
2.03-2.090.2181410.20777312X-RAY DIFFRACTION100
2.09-2.160.2551430.19697355X-RAY DIFFRACTION100
2.16-2.230.22691410.18327292X-RAY DIFFRACTION100
2.23-2.320.23031420.17187325X-RAY DIFFRACTION100
2.32-2.430.21081430.16737367X-RAY DIFFRACTION100
2.43-2.560.19891430.16287368X-RAY DIFFRACTION100
2.56-2.720.18921410.16687343X-RAY DIFFRACTION100
2.72-2.930.20521430.17217387X-RAY DIFFRACTION100
2.93-3.220.21211440.18167424X-RAY DIFFRACTION100
3.22-3.690.21440.17437428X-RAY DIFFRACTION100
3.69-4.640.15541450.15147487X-RAY DIFFRACTION100
4.64-25.010.20551490.16637684X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 46.1781 Å / Origin y: 39.9869 Å / Origin z: 69.9577 Å
111213212223313233
T0.424 Å2-0.0021 Å20.002 Å2-0.2496 Å2-0.013 Å2--0.1663 Å2
L0.5056 °2-0.0637 °2-0.0013 °2-0.4569 °2-0.0616 °2--0.8365 °2
S-0.0165 Å °0.0329 Å °0.0028 Å °-0.0064 Å °0.0014 Å °0.0492 Å °-0.0756 Å °-0.1355 Å °0.0142 Å °
Refinement TLS groupSelection details: all

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