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- PDB-1is2: Crystal Structure of Peroxisomal Acyl-CoA Oxidase-II from Rat Liver -

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Basic information

Entry
Database: PDB / ID: 1is2
TitleCrystal Structure of Peroxisomal Acyl-CoA Oxidase-II from Rat Liver
Componentsacyl-CoA oxidase
KeywordsOXIDOREDUCTASE / FAD
Function / homology
Function and homology information


very long-chain fatty acid beta-oxidation / : / alpha-linolenic acid (ALA) metabolism / acyl-CoA oxidase / Beta-oxidation of very long chain fatty acids / acyl-CoA oxidase activity / Peroxisomal protein import / fatty acid beta-oxidation using acyl-CoA oxidase / fatty acid derivative biosynthetic process / alpha-linolenic acid metabolic process ...very long-chain fatty acid beta-oxidation / : / alpha-linolenic acid (ALA) metabolism / acyl-CoA oxidase / Beta-oxidation of very long chain fatty acids / acyl-CoA oxidase activity / Peroxisomal protein import / fatty acid beta-oxidation using acyl-CoA oxidase / fatty acid derivative biosynthetic process / alpha-linolenic acid metabolic process / very long-chain fatty acid metabolic process / unsaturated fatty acid biosynthetic process / fatty acid catabolic process / hydrogen peroxide biosynthetic process / peroxisomal membrane / long-chain fatty acid biosynthetic process / prostaglandin metabolic process / fatty acid oxidation / peroxisomal matrix / FAD binding / fatty acid binding / generation of precursor metabolites and energy / PDZ domain binding / lipid metabolic process / peroxisome / flavin adenine dinucleotide binding / spermatogenesis / protein homodimerization activity / cytoplasm
Similarity search - Function
Peroxisomal acyl-coenzyme A oxidase / : / 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 ...Peroxisomal acyl-coenzyme A oxidase / : / 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/dehydrogenase, middle domain / 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
FLAVIN-ADENINE DINUCLEOTIDE / Peroxisomal acyl-coenzyme A oxidase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsNakajima, Y. / Miyahara, I. / Hirotsu, K.
CitationJournal: J.Biochem. / Year: 2002
Title: Three-dimensional structure of the flavoenzyme acyl-CoA oxidase-II from rat liver, the peroxisomal counterpart of mitochondrial acyl-CoA dehydrogenase.
Authors: Nakajima, Y. / Miyahara, I. / Hirotsu, K. / Nishina, Y. / Shiga, K. / Setoyama, C. / Tamaoki, H. / Miura, R.
History
DepositionNov 7, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: acyl-CoA oxidase
B: acyl-CoA oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,1404
Polymers149,5692
Non-polymers1,5712
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13050 Å2
ΔGint-70 kcal/mol
Surface area45350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.030, 91.501, 214.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein acyl-CoA oxidase


Mass: 74784.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / References: UniProt: P07872, acyl-CoA oxidase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 20000, potassium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.0 mg/mlprotein1drop
23.0 %(w/v)PEG200001drop
320 mMpotassium phosphate1droppH7.4
48-11 %(w/v)PEG200001reservoir
5100 mMpotassium phosphate1reservoirpH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 69647 / Num. obs: 69647 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 2.1 / Num. unique all: 6152 / % possible all: 85.3
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 344046 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 85.3 % / Num. unique obs: 6152 / Num. measured obs: 22267 / Rmerge(I) obs: 0.283

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→10 Å / σ(F): 2 / Stereochemistry target values: RANDOM
RfactorNum. reflection% reflectionSelection details
Rfree0.26 6806 10.13 %RANDOM
Rwork0.209 ---
all-68689 --
obs-67164 93.3 %-
Displacement parametersBiso mean: 32.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9939 0 106 443 10488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.252
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d0.834
X-RAY DIFFRACTIONc_mcbond_it1.294
X-RAY DIFFRACTIONc_mcangle_it1.979
Refinement
*PLUS
Rfactor obs: 0.209 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.834

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