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- PDB-5k3h: Crystals structure of Acyl-CoA oxidase-1 in Caenorhabditis elegan... -

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Basic information

Entry
Database: PDB / ID: 5k3h
TitleCrystals structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans, Apo form-II
ComponentsAcyl-coenzyme A oxidase
KeywordsOXIDOREDUCTASE / dauer pheromone / ascarosides / b-oxidation / ATP
Function / homology
Function and homology information


ascaroside biosynthetic process / Beta-oxidation of pristanoyl-CoA / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Oxidoreductases; Acting on the CH-CH group of donors; With oxygen as acceptor / acyl-CoA oxidase / Peroxisomal protein import / acyl-CoA oxidase activity / pheromone biosynthetic process / fatty acid beta-oxidation using acyl-CoA oxidase / lipid homeostasis ...ascaroside biosynthetic process / Beta-oxidation of pristanoyl-CoA / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Oxidoreductases; Acting on the CH-CH group of donors; With oxygen as acceptor / acyl-CoA oxidase / Peroxisomal protein import / 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 / 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
Acyl-coenzyme A oxidase acox-1.1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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
E: Acyl-coenzyme A oxidase
F: Acyl-coenzyme A oxidase
G: Acyl-coenzyme A oxidase
H: Acyl-coenzyme A oxidase


Theoretical massNumber of molelcules
Total (without water)620,4638
Polymers620,4638
Non-polymers00
Water26,5901476
1
A: Acyl-coenzyme A oxidase
B: Acyl-coenzyme A oxidase


Theoretical massNumber of molelcules
Total (without water)155,1162
Polymers155,1162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-61 kcal/mol
Surface area47390 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-61 kcal/mol
Surface area47750 Å2
MethodPISA
3
E: Acyl-coenzyme A oxidase
F: Acyl-coenzyme A oxidase


Theoretical massNumber of molelcules
Total (without water)155,1162
Polymers155,1162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-61 kcal/mol
Surface area47480 Å2
MethodPISA
4
G: Acyl-coenzyme A oxidase
H: Acyl-coenzyme A oxidase


Theoretical massNumber of molelcules
Total (without water)155,1162
Polymers155,1162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-60 kcal/mol
Surface area47580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.075, 140.795, 154.930
Angle α, β, γ (deg.)90.00, 117.20, 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.: 8
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1476 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
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: 2.48→49.241 Å / Num. obs: 206114 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.14 / Net I/σ(I): 14.4
Reflection shellResolution: 2.48→2.52 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 0.66 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IS2

1is2


Resolution: 2.48→49.241 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.43 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2315 10166 4.93 %
Rwork0.1907 --
obs0.1932 206114 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→49.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40266 0 0 1476 41742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941093
X-RAY DIFFRACTIONf_angle_d1.04555557
X-RAY DIFFRACTIONf_dihedral_angle_d12.95224829
X-RAY DIFFRACTIONf_chiral_restr0.0596190
X-RAY DIFFRACTIONf_plane_restr0.0077144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.52280.28014700.23599478X-RAY DIFFRACTION92
2.5228-2.56870.29685190.2329769X-RAY DIFFRACTION95
2.5687-2.61810.26765200.22349745X-RAY DIFFRACTION95
2.6181-2.67150.30644840.21989840X-RAY DIFFRACTION95
2.6715-2.72960.26974710.22019767X-RAY DIFFRACTION95
2.7296-2.7930.28135190.22019797X-RAY DIFFRACTION95
2.793-2.86290.28285120.21389811X-RAY DIFFRACTION95
2.8629-2.94020.24895460.21629697X-RAY DIFFRACTION95
2.9402-3.02670.25865760.21079727X-RAY DIFFRACTION94
3.0267-3.12440.2595050.20539810X-RAY DIFFRACTION95
3.1244-3.2360.26644380.19579862X-RAY DIFFRACTION96
3.236-3.36550.24154640.1919842X-RAY DIFFRACTION95
3.3655-3.51860.20444820.18039827X-RAY DIFFRACTION95
3.5186-3.70390.21425200.17819791X-RAY DIFFRACTION95
3.7039-3.93580.19755170.16959810X-RAY DIFFRACTION95
3.9358-4.23930.19335100.16189822X-RAY DIFFRACTION95
4.2393-4.66530.17454730.15729868X-RAY DIFFRACTION95
4.6653-5.33880.20845670.1739824X-RAY DIFFRACTION95
5.3388-6.72050.24336060.20199798X-RAY DIFFRACTION94
6.7205-38.52130.21293760.183210123X-RAY DIFFRACTION96

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