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- PDB-5k3j: Crystals structure of Acyl-CoA oxidase-2 in Caenorhabditis elegan... -

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Basic information

Entry
Database: PDB / ID: 5k3j
TitleCrystals structure of Acyl-CoA oxidase-2 in Caenorhabditis elegans bound with FAD, ascaroside-CoA, and ATP
ComponentsAcyl-coenzyme A oxidase
KeywordsOXIDOREDUCTASE / dauer pheromone / ascarosides / b-oxidation / ATP / crystal structure
Function / homology
Function and homology information


ascaroside biosynthetic process / Beta-oxidation of pristanoyl-CoA / Oxidoreductases; Acting on the CH-CH group of donors; With oxygen as acceptor / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Peroxisomal protein import / acyl-CoA oxidase activity / fatty acid beta-oxidation using acyl-CoA oxidase / lipid homeostasis / FAD binding / fatty acid binding ...ascaroside biosynthetic process / Beta-oxidation of pristanoyl-CoA / Oxidoreductases; Acting on the CH-CH group of donors; With oxygen as acceptor / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Peroxisomal protein import / acyl-CoA oxidase activity / fatty acid beta-oxidation using acyl-CoA oxidase / lipid homeostasis / FAD binding / fatty acid binding / peroxisome / flavin adenine dinucleotide binding / ATP binding
Similarity search - Function
Acyl-CoA oxidase, C-terminal / Acyl-CoA oxidase / Acyl-coenzyme A oxidase, N-terminal / Acyl-CoA oxidase / Acyl-coenzyme A oxidase N-terminal / Acyl-CoA oxidase, C-alpha1 domain / 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 oxidase, C-terminal / Acyl-CoA oxidase / Acyl-coenzyme A oxidase, N-terminal / Acyl-CoA oxidase / Acyl-coenzyme A oxidase N-terminal / Acyl-CoA oxidase, C-alpha1 domain / 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, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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
Chem-6QA / ADENOSINE-5'-TRIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Acyl-coenzyme A oxidase acox-1.2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsZhang, X. / Li, K. / Jones, R.A. / Bruner, S.D. / Butcher, R.A.
Funding support United States, 4items
OrganizationGrant numberCountry
Research Corporation for Science Advancement22844 United States
Ellison Medical FoundationAG-NS-0963-12 United States
National Science Foundation (NSF, United States)1555050 United States
Alfred P. Sloan FoundationBR2014-071 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural characterization of acyl-CoA oxidases reveals a direct link between pheromone biosynthesis and metabolic state in Caenorhabditis elegans.
Authors: Zhang, X. / Li, K. / Jones, R.A. / Bruner, S.D. / Butcher, R.A.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-coenzyme A oxidase
B: Acyl-coenzyme A oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,09510
Polymers153,4662
Non-polymers4,6308
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16860 Å2
ΔGint-106 kcal/mol
Surface area44580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.040, 85.571, 106.899
Angle α, β, γ (deg.)90.00, 91.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acyl-coenzyme A oxidase


Mass: 76732.891 Da / Num. of mol.: 2 / Mutation: E432A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: acox-2, CELE_F08A8.2, F08A8.2 / Plasmid: pET16b / Details (production host): Cterm fused octa-histag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O62137

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Non-polymers , 5 types, 171 molecules

#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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-6QA / ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-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]ethyl] 5-[(2~{R},3~{R},5~{R},6~{S})-6-methyl-3,5-bis(oxidanyl)oxan-2-yl]oxypentanethioate


Mass: 997.792 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H54N7O21P3S
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.27 Å3/Da / Density % sol: 45.71 % / Description: plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 0.2 M ammonium acetate, 0.1 M Tris-HCl pH 8.5 and 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.68→39.72 Å / Num. obs: 38639 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.16 / Rsym value: 0.2 / Net I/σ(I): 10.9
Reflection shellResolution: 2.68→2.8 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Acox1a

Resolution: 2.68→39.72 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.97 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2452 1972 5.11 %
Rwork0.2132 --
obs0.2149 38624 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10518 0 298 163 10979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411047
X-RAY DIFFRACTIONf_angle_d0.93114970
X-RAY DIFFRACTIONf_dihedral_angle_d17.0944168
X-RAY DIFFRACTIONf_chiral_restr0.0321641
X-RAY DIFFRACTIONf_plane_restr0.0041876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6803-2.74730.42091350.29972576X-RAY DIFFRACTION95
2.7473-2.82150.37871370.28552649X-RAY DIFFRACTION95
2.8215-2.90440.33871300.2692571X-RAY DIFFRACTION95
2.9044-2.99810.3181470.26752602X-RAY DIFFRACTION95
2.9981-3.10510.31341220.26322642X-RAY DIFFRACTION96
3.1051-3.22920.29961490.24432584X-RAY DIFFRACTION94
3.2292-3.37590.27051540.24032581X-RAY DIFFRACTION94
3.3759-3.55360.26061140.22152662X-RAY DIFFRACTION96
3.5536-3.77570.27031410.21762603X-RAY DIFFRACTION95
3.7757-4.06640.21881180.19232642X-RAY DIFFRACTION96
4.0664-4.4740.22651610.1792615X-RAY DIFFRACTION94
4.474-5.11780.20161490.17782592X-RAY DIFFRACTION94
5.1178-6.43440.19571380.19072642X-RAY DIFFRACTION95
6.4344-27.56030.16131430.16192690X-RAY DIFFRACTION94

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