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- PDB-8r1e: crystal structure of acyl-CoA dehydrogenase FadE2 mutant (PA0508 ... -

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Basic information

Entry
Database: PDB / ID: 8r1e
Titlecrystal structure of acyl-CoA dehydrogenase FadE2 mutant (PA0508 M130G E296A Q303A) from Pseudomonas aeruginosa
ComponentsProbable acyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / acyl-CoA dehydrogenase / beta-oxidation
Function / homology
Function and homology information


3-(methylsulfanyl)propanoyl-CoA 2-dehydrogenase / oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenase, N-terminal, bacteria / : / Acetyl-CoA dehydrogenase-like C-terminal domain / Acetyl-CoA dehydrogenase C-terminal like / : / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain ...Acyl-CoA dehydrogenase, N-terminal, bacteria / : / Acetyl-CoA dehydrogenase-like C-terminal domain / Acetyl-CoA dehydrogenase C-terminal like / : / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / 3-methylmercaptopropionyl-CoA dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsWang, M. / Brear, P. / Welch, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cystic Fibrosis TrustSRC017 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Pseudomonas aeruginosa acyl-CoA dehydrogenases and structure-guided inversion of their substrate specificity.
Authors: Wang, M. / Medarametla, P. / Kronenberger, T. / Deingruber, T. / Brear, P. / Figueroa, W. / Ho, P.M. / Krueger, T. / Pearce, J.C. / Poso, A. / Wakefield, J.G. / Spring, D.R. / Welch, M.
History
DepositionNov 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Probable acyl-CoA dehydrogenase
A: Probable acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,3968
Polymers127,3992
Non-polymers1,9986
Water15,349852
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-60 kcal/mol
Surface area38630 Å2
Unit cell
Length a, b, c (Å)61.892, 64.756, 287.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable acyl-CoA dehydrogenase


Mass: 63699.270 Da / Num. of mol.: 2 / Mutation: M130G E296A Q303A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA0508 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I610
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 852 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% (w/v) PEG 1500 ; 0.1 M PCB (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.62→71.99 Å / Num. obs: 147729 / % possible obs: 99.76 % / Redundancy: 12.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.042 / Rrim(I) all: 0.15 / Net I/σ(I): 9.7
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 6 % / Rmerge(I) obs: 2.632 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 6871 / CC1/2: 0.31 / Rpim(I) all: 1.143 / Rrim(I) all: 2.884 / % possible all: 94.93

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8PNG

8png


Resolution: 1.62→71.99 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.68 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22358 2005 1.4 %RANDOM
Rwork0.19135 ---
obs0.19181 144075 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.605 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2--3.51 Å2-0 Å2
3----2.37 Å2
Refinement stepCycle: 1 / Resolution: 1.62→71.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8930 0 134 852 9916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139261
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158728
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.63712560
X-RAY DIFFRACTIONr_angle_other_deg1.4161.57420076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93551183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17622.096439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.777151470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7921556
X-RAY DIFFRACTIONr_chiral_restr0.0750.21198
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210585
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022081
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_it1.8922.8324738
X-RAY DIFFRACTIONr_mcbond_other1.8922.8324737
X-RAY DIFFRACTIONr_mcangle_it2.5514.245919
X-RAY DIFFRACTIONr_mcangle_other2.5514.245920
X-RAY DIFFRACTIONr_scbond_it2.9283.1534523
X-RAY DIFFRACTIONr_scbond_other2.9283.1544524
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4144.66642
X-RAY DIFFRACTIONr_long_range_B_refined5.49434.72111047
X-RAY DIFFRACTIONr_long_range_B_other5.42434.31910813
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.503 117 -
Rwork0.499 8950 -
obs--83.9 %

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