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- PDB-5ys9: Crystal structure of acyl-coA oxidase3 from Yarrowia lipolytica -

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Basic information

Entry
Database: PDB / ID: 5ys9
TitleCrystal structure of acyl-coA oxidase3 from Yarrowia lipolytica
ComponentsAcyl-coenzyme A oxidase 3
KeywordsOXIDOREDUCTASE / FAD-binding protein
Function / homology
Function and homology information


acyl-CoA oxidase / acyl-CoA oxidase activity / fatty acid beta-oxidation using acyl-CoA oxidase / lipid homeostasis / FAD binding / fatty acid binding / peroxisome / flavin adenine dinucleotide 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 / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily ...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 / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Acyl-coenzyme A oxidase 3
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsKim, S. / Kim, K.-J.
CitationJournal: J. Microbiol. Biotechnol. / Year: 2018
Title: Crystal Structure of Acyl-CoA Oxidase 3 fromYarrowia lipolyticawith Specificity for Short-Chain Acyl-CoA.
Authors: Kim, S. / Kim, K.J.
History
DepositionNov 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: Acyl-coenzyme A oxidase 3
B: Acyl-coenzyme A oxidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,9184
Polymers158,3472
Non-polymers1,5712
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14290 Å2
ΔGint-72 kcal/mol
Surface area52200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.824, 160.824, 139.467
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Acyl-coenzyme A oxidase 3 / Acyl-CoA oxidase 3


Mass: 79173.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (strain CLIB 122 / E 150) (yeast)
Strain: CLIB 122 / E 150 / Gene: POX3, ACO3, YALI0D24750g / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O74936, 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.: 168 / 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: 2.85 Å3/Da / Density % sol: 56.81 % / Mosaicity: 1.125 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Pentaerythritol propoxylate, KCl, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 28, 2015 / Details: Rh coated Torroidal Mirror
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 60127 / % possible obs: 98.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.076 / Χ2: 2.621 / Net I/σ(I): 20.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.544.30.28129220.8890.1450.3181.71198
2.54-2.594.30.26330240.8950.1350.2971.72298.3
2.59-2.644.50.23929690.9250.120.2681.74998.6
2.64-2.694.50.2330040.9230.1160.2591.85698.6
2.69-2.754.50.20229640.9480.10.2261.81298.4
2.75-2.824.70.18729870.960.090.2082.03497.9
2.82-2.894.80.17529940.9630.0830.1942.09698.8
2.89-2.964.90.15330030.9750.0720.172.18598.4
2.96-3.055.10.13429460.9810.0620.1482.21898
3.05-3.155.30.12430160.9840.0560.1362.40698.6
3.15-3.265.40.11229910.9870.050.1232.64798.4
3.26-3.395.80.09530090.9930.0410.1032.93998.8
3.39-3.5560.08229990.9940.0350.093.06299
3.55-3.736.20.07230450.9960.030.0783.14399.3
3.73-3.976.30.06430000.9970.0260.0693.41799
3.97-4.276.50.05630220.9970.0230.0613.53799
4.27-4.76.60.05230190.9980.0210.0563.50499.2
4.7-5.386.60.04930530.9980.020.0533.04199.7
5.38-6.786.70.04730590.9980.0190.0512.60599.8
6.78-506.70.03931010.9990.0160.0422.58399.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 5Y9D

5y9d


Resolution: 2.5→35.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.581 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.255
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 3044 5.1 %RANDOM
Rwork0.1807 ---
obs0.1829 57083 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 146.17 Å2 / Biso mean: 45.449 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å2-0 Å2
2---0.17 Å2-0 Å2
3---0.33 Å2
Refinement stepCycle: final / Resolution: 2.5→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10855 0 106 168 11129
Biso mean--48 38.52 -
Num. residues----1383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01911209
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210543
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.96215187
X-RAY DIFFRACTIONr_angle_other_deg0.883324241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26851381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78324.16524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.969151890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7141570
X-RAY DIFFRACTIONr_chiral_restr0.10.21637
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022639
LS refinement shellResolution: 2.504→2.569 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 212 -
Rwork0.193 4128 -
all-4340 -
obs--96.72 %

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