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- PDB-8pu5: Crystal structure of the Acyl-CoA dehydrogenase FadE1(PA0506) E44... -

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Basic information

Entry
Database: PDB / ID: 8pu5
TitleCrystal structure of the Acyl-CoA dehydrogenase FadE1(PA0506) E441A from Pseudomonas aeruginosa complexed with C16CoA
ComponentsProbable acyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / acyl-CoA dehydrogenase / beta-oxidation
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenase, N-terminal, bacteria / Acyl-CoA dehydrogenase N terminal / 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 / Acyl-CoA dehydrogenase N terminal / 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
NITRATE ION / TRIETHYLENE GLYCOL / Palmitoyl-CoA / Probable acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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
DepositionJul 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 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

Downloads & links

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Assembly

Deposited unit
B: Probable acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,21810
Polymers65,5681
Non-polymers1,6519
Water7,440413
1
B: Probable acyl-CoA dehydrogenase
hetero molecules

B: Probable acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,43620
Polymers131,1352
Non-polymers3,30118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
Buried area13370 Å2
ΔGint3 kcal/mol
Surface area40080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.955, 92.955, 128.782
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11B-1185-

HOH

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Probable acyl-CoA dehydrogenase


Mass: 65567.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA0506 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: Q9I612

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Non-polymers , 6 types, 422 molecules

#2: Chemical ChemComp-PKZ / Palmitoyl-CoA


Mass: 1005.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H66N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis Tris Propane pH 6.5, 0.2M sodium nitrate, 20% w/v PEG 3350, 10% v/v ethylene glycol, 5mM C16CoA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.44→128.78 Å / Num. obs: 114956 / % possible obs: 100 % / Redundancy: 38.5 % / Biso Wilson estimate: 15.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.031 / Rrim(I) all: 0.197 / Net I/σ(I): 11.5
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 29.3 % / Rmerge(I) obs: 4.451 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 5683 / CC1/2: 0.3 / Rpim(I) all: 0.834 / Rrim(I) all: 4.529 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHASERphasing
xia23.3.3data scaling
xia23.3.3data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→80.63 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.01 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21378 5767 5 %RANDOM
Rwork0.18462 ---
obs0.1861 109044 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å2-0 Å2
2---0.32 Å20 Å2
3---1.02 Å2
Refinement stepCycle: 1 / Resolution: 1.44→80.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4563 0 107 421 5091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134824
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164546
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.6466510
X-RAY DIFFRACTIONr_angle_other_deg1.5061.57510484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9315612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73122.7237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71115793
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0081525
X-RAY DIFFRACTIONr_chiral_restr0.0870.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021085
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_it1.6322.1342415
X-RAY DIFFRACTIONr_mcbond_other1.6312.1342414
X-RAY DIFFRACTIONr_mcangle_it2.2893.1973023
X-RAY DIFFRACTIONr_mcangle_other2.2893.1973024
X-RAY DIFFRACTIONr_scbond_it3.0042.4972405
X-RAY DIFFRACTIONr_scbond_other3.0032.4952400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4493.6093473
X-RAY DIFFRACTIONr_long_range_B_refined5.70626.6765512
X-RAY DIFFRACTIONr_long_range_B_other5.59626.2055436
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 393 -
Rwork0.375 8004 -
obs--99.03 %

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