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- PDB-5k3g: Crystals structure of Acyl-CoA oxidase-1 in Caenorhabditis elegan... -

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Basic information

Entry
Database: PDB / ID: 5k3g
TitleCrystals structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans, Apo form-I
ComponentsAcyl-coenzyme A oxidase
KeywordsOXIDOREDUCTASE / dauer pheromone / ascarosides / b-oxidation / ATP
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With oxygen as acceptor / Beta-oxidation of pristanoyl-CoA / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Peroxisomal protein import / ascaroside biosynthetic process / acyl-CoA oxidase / acyl-CoA oxidase activity / pheromone biosynthetic process / fatty acid beta-oxidation using acyl-CoA oxidase / lipid homeostasis ...Oxidoreductases; Acting on the CH-CH group of donors; With oxygen as acceptor / Beta-oxidation of pristanoyl-CoA / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Peroxisomal protein import / ascaroside biosynthetic process / acyl-CoA oxidase / acyl-CoA oxidase activity / pheromone biosynthetic process / fatty acid beta-oxidation using acyl-CoA oxidase / lipid homeostasis / peroxisomal matrix / 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 / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 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
Acyl-coenzyme A oxidase acox-1.1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.859 Å
AuthorsZhang, X. / Li, K. / Jones, R.A. / Bruner, S.D. / Butcher, R.A.
Funding support United States, 5items
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087533 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 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-coenzyme A oxidase
B: Acyl-coenzyme A oxidase
C: Acyl-coenzyme A oxidase
D: Acyl-coenzyme A oxidase


Theoretical massNumber of molelcules
Total (without water)310,2314
Polymers310,2314
Non-polymers00
Water00
1
A: Acyl-coenzyme A oxidase
B: Acyl-coenzyme A oxidase


Theoretical massNumber of molelcules
Total (without water)155,1162
Polymers155,1162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-63 kcal/mol
Surface area47680 Å2
MethodPISA
2
C: Acyl-coenzyme A oxidase
D: Acyl-coenzyme A oxidase


Theoretical massNumber of molelcules
Total (without water)155,1162
Polymers155,1162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-65 kcal/mol
Surface area47850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.433, 140.547, 131.335
Angle α, β, γ (deg.)90.00, 91.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acyl-coenzyme A oxidase


Mass: 77557.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: acox-1, CELE_F08A8.1, F08A8.1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O62140

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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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.4 M NaCl, 0.1 M HEPES pH 7.4, 18% w/v PEG 8000 and 8% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 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: 2.859→48.851 Å / Num. obs: 67386 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.16 / Net I/σ(I): 12.2
Reflection shellResolution: 2.859→2.96 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 0.61 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IS2

1is2


Resolution: 2.859→48.851 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.39
RfactorNum. reflection% reflection
Rfree0.226 3624 5.38 %
Rwork0.2156 --
obs0.2169 67380 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.859→48.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20012 0 0 0 20012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00420458
X-RAY DIFFRACTIONf_angle_d0.79527656
X-RAY DIFFRACTIONf_dihedral_angle_d13.58612352
X-RAY DIFFRACTIONf_chiral_restr0.0463081
X-RAY DIFFRACTIONf_plane_restr0.0053552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8609-2.91020.30121450.27343167X-RAY DIFFRACTION95
2.9102-2.9630.24871620.24493191X-RAY DIFFRACTION95
2.963-3.01980.28741620.253147X-RAY DIFFRACTION95
3.0198-3.08140.26761760.24443221X-RAY DIFFRACTION95
3.0814-3.14820.27941850.23753145X-RAY DIFFRACTION94
3.1482-3.22130.2652110.23653170X-RAY DIFFRACTION94
3.2213-3.30160.26591790.23373149X-RAY DIFFRACTION95
3.3016-3.39060.25691700.22653184X-RAY DIFFRACTION95
3.3906-3.49010.27472010.24763190X-RAY DIFFRACTION94
3.4901-3.60230.2361590.22413165X-RAY DIFFRACTION95
3.6023-3.73060.25721810.22983167X-RAY DIFFRACTION94
3.7306-3.87930.21251740.20783201X-RAY DIFFRACTION95
3.8793-4.0550.22111760.21393156X-RAY DIFFRACTION95
4.055-4.26760.21051810.19483209X-RAY DIFFRACTION95
4.2676-4.53320.17071750.18263165X-RAY DIFFRACTION95
4.5332-4.88030.20351830.19643201X-RAY DIFFRACTION95
4.8803-5.3660.20391640.20193210X-RAY DIFFRACTION95
5.366-6.13030.27241930.22553169X-RAY DIFFRACTION94
6.1303-7.67810.22951650.21393229X-RAY DIFFRACTION95
7.6781-23.42530.15642560.17293187X-RAY DIFFRACTION93

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