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- PDB-5k3i: Crystal structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans... -

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Basic information

Entry
Database: PDB / ID: 5k3i
TitleCrystal structure of Acyl-CoA oxidase-1 in Caenorhabditis elegans complexed with FAD and ATP
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
ADENOSINE-5'-TRIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / Acyl-coenzyme A oxidase acox-1.1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.683 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.6Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / refine
Item: _pdbx_initial_refinement_model.accession_code / _refine.pdbx_starting_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)630,53532
Polymers619,9998
Non-polymers10,53624
Water10,827601
1
A: Acyl-coenzyme A oxidase
B: Acyl-coenzyme A oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,6348
Polymers155,0002
Non-polymers2,6346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16940 Å2
ΔGint-108 kcal/mol
Surface area45700 Å2
MethodPISA
2
C: Acyl-coenzyme A oxidase
D: Acyl-coenzyme A oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,6348
Polymers155,0002
Non-polymers2,6346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17020 Å2
ΔGint-111 kcal/mol
Surface area44780 Å2
MethodPISA
3
E: Acyl-coenzyme A oxidase
F: Acyl-coenzyme A oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,6348
Polymers155,0002
Non-polymers2,6346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16860 Å2
ΔGint-107 kcal/mol
Surface area45220 Å2
MethodPISA
4
G: Acyl-coenzyme A oxidase
H: Acyl-coenzyme A oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,6348
Polymers155,0002
Non-polymers2,6346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16960 Å2
ΔGint-110 kcal/mol
Surface area45150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.339, 141.501, 154.968
Angle α, β, γ (deg.)90.00, 116.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acyl-coenzyme A oxidase


Mass: 77499.820 Da / Num. of mol.: 8 / Mutation: E434A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: acox-1, CELE_F08A8.1, F08A8.1 / Production host: Escherichia coli (E. coli) / References: UniProt: O62140
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 49.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.4 M NaCl, 0.1 M HEPES pH 7.4, 18% w/v PEG 8000 and 8% v/v glycerol
PH range: 7.4

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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: Mar 13, 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: 2.63→38.736 Å / Num. obs: 163296 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.17 / Net I/σ(I): 8.4
Reflection shellResolution: 2.63→2.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 0.7 / % possible all: 98.3

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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: 5K3G

5k3g


Resolution: 2.683→38.736 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.56 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2321 8124 4.98 %
Rwork0.2169 --
obs0.2176 163296 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.683→38.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41619 0 680 601 42900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00843305
X-RAY DIFFRACTIONf_angle_d0.98358644
X-RAY DIFFRACTIONf_dihedral_angle_d14.24125970
X-RAY DIFFRACTIONf_chiral_restr0.0556488
X-RAY DIFFRACTIONf_plane_restr0.0067409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6833-2.72960.3063990.29087410X-RAY DIFFRACTION91
2.7296-2.77920.31994210.28247716X-RAY DIFFRACTION95
2.7792-2.83260.28663810.26787781X-RAY DIFFRACTION95
2.8326-2.89040.3083680.26817782X-RAY DIFFRACTION95
2.8904-2.95320.2874040.26097724X-RAY DIFFRACTION95
2.9532-3.02190.28883390.25667860X-RAY DIFFRACTION96
3.0219-3.09740.25673710.24447811X-RAY DIFFRACTION95
3.0974-3.18110.26364030.24127718X-RAY DIFFRACTION95
3.1811-3.27460.23313600.23777816X-RAY DIFFRACTION95
3.2746-3.38020.26594090.22947779X-RAY DIFFRACTION95
3.3802-3.50090.25014280.22467722X-RAY DIFFRACTION95
3.5009-3.6410.23054300.22197724X-RAY DIFFRACTION95
3.641-3.80650.22344520.21447729X-RAY DIFFRACTION94
3.8065-4.00690.20974330.20227741X-RAY DIFFRACTION95
4.0069-4.25750.21843810.19247812X-RAY DIFFRACTION95
4.2575-4.58550.19364170.1797800X-RAY DIFFRACTION95
4.5855-5.04570.19643890.18397810X-RAY DIFFRACTION95
5.0457-5.77280.21654230.20987794X-RAY DIFFRACTION95
5.7728-7.26170.22694210.20877815X-RAY DIFFRACTION95
7.2617-34.27570.17413860.16047913X-RAY DIFFRACTION94

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