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- PDB-8pns: Crystal structure of the acyl-CoA dehydrogenase PA0506 (FadE1) fr... -

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Basic information

Entry
Database: PDB / ID: 8pns
TitleCrystal structure of the acyl-CoA dehydrogenase PA0506 (FadE1) from Pseudomonas aeruginosa
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / acyl-CoA dehydrogenase / beta-oxidation
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / short-chain fatty acyl-CoA dehydrogenase activity / 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
OCTANOYL-COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsWang, M. / Brear, P. / Welch, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cystic Fibrosis TrustSRC01 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
DepositionJun 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 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
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,8228
Polymers131,2512
Non-polymers3,5716
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Analytic ultracentrifuge indicated that it is dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16150 Å2
ΔGint-51 kcal/mol
Surface area39630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.918, 155.918, 99.511
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Acyl-CoA dehydrogenase


Mass: 65625.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: mmgC10, ALP65_01436, CAZ10_18495, CGU42_20105, GNQ48_07395, GUL26_18035, NCTC13621_06274, PA52Ts2_5823
Production host: Escherichia coli (E. coli)
References: UniProt: A0A072ZR57, short-chain acyl-CoA dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CO8 / OCTANOYL-COENZYME A


Mass: 893.730 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H50N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES pH6, 0.1M Calcium chloride dihydrate, 20% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.08→135.03 Å / Num. obs: 82487 / % possible obs: 100 % / Redundancy: 15.9 % / Biso Wilson estimate: 26.61 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.238 / Rpim(I) all: 0.061 / Rrim(I) all: 0.246 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible allMean I/σ(I) obs
3.56-3.9216.90.13841170.9960.0340.142100
3-3.560.19241450.9930.0470.19810012.2
2.82-2.9518.050.42741250.9690.1030.4391004.7
2.08-2.1211.122.940380.370.9053.04199.170.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→135.03 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.293 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24872 4059 4.9 %RANDOM
Rwork0.20392 ---
obs0.20617 78359 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: 40.223 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å20 Å2
2--0.68 Å2-0 Å2
3----2.2 Å2
Refinement stepCycle: 1 / Resolution: 2.08→135.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9141 0 234 146 9521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139610
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158936
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.64413013
X-RAY DIFFRACTIONr_angle_other_deg1.3361.57520588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75551201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17522.7474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.062151558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2361550
X-RAY DIFFRACTIONr_chiral_restr0.0810.21223
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022175
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_it3.2424.0984804
X-RAY DIFFRACTIONr_mcbond_other3.2424.0984803
X-RAY DIFFRACTIONr_mcangle_it4.5586.1416005
X-RAY DIFFRACTIONr_mcangle_other4.5576.1416006
X-RAY DIFFRACTIONr_scbond_it4.1424.4874806
X-RAY DIFFRACTIONr_scbond_other4.1424.4874807
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0936.5997009
X-RAY DIFFRACTIONr_long_range_B_refined7.6148.59210787
X-RAY DIFFRACTIONr_long_range_B_other7.60848.59410777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 285 -
Rwork0.367 5723 -
obs--99.11 %

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