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- PDB-7q86: Crystal structure of human peroxisomal acyl-Co-A oxidase 1a, FAD-... -

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Basic information

Entry
Database: PDB / ID: 7q86
TitleCrystal structure of human peroxisomal acyl-Co-A oxidase 1a, FAD-bound-form
ComponentsIsoform 2 of Peroxisomal acyl-coenzyme A oxidase 1
KeywordsOXIDOREDUCTASE / acyl-Co-A oxidase / peroxisomal enzyme
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsSonani, R.R. / Blat, A. / Dubin, G.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/M/NZ1/00797 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Crystal structures of apo- and FAD-bound human peroxisomal acyl-CoA oxidase provide mechanistic basis explaining clinical observations.
Authors: Sonani, R.R. / Blat, A. / Dubin, G.
History
DepositionNov 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Peroxisomal acyl-coenzyme A oxidase 1
B: Isoform 2 of Peroxisomal acyl-coenzyme A oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,0784
Polymers151,5072
Non-polymers1,5712
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-63 kcal/mol
Surface area44730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.961, 124.063, 142.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isoform 2 of Peroxisomal acyl-coenzyme A oxidase 1


Mass: 75753.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACOX1, ACOX / Production host: Escherichia coli (E. coli) / References: acyl-CoA oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 12.5 % PEG 8000, 0.09 M ammonium sulfate, 0.05 M sodium cacodylate (pH 6.0) + Soaking in 0.5 mM FAD

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.09→47.84 Å / Num. obs: 79500 / % possible obs: 99.85 % / Redundancy: 7.3 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.04 / Rrim(I) all: 0.11 / Net I/σ(I): 16.77
Reflection shellResolution: 2.09→2.165 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.207 / Num. unique obs: 7854 / CC1/2: 0.639 / CC star: 0.883 / Rpim(I) all: 0.04 / Rrim(I) all: 0.11 / % possible all: 99.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Q84

7q84


Resolution: 2.09→47.84 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.17 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2398 4054 5.1 %RANDOM
Rwork0.1872 ---
obs0.19 75433 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.41 Å2 / Biso mean: 46.884 Å2 / Biso min: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.39 Å20 Å20 Å2
2---1.3 Å20 Å2
3----2.09 Å2
Refinement stepCycle: final / Resolution: 2.09→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9718 0 106 395 10219
Biso mean--35.09 38.85 -
Num. residues----1219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01310058
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179533
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.64613626
X-RAY DIFFRACTIONr_angle_other_deg1.4511.57621941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76551210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65322.034526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.334151740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5381566
X-RAY DIFFRACTIONr_chiral_restr0.0950.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211252
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022326
LS refinement shellResolution: 2.09→2.144 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 296 -
Rwork0.305 5534 -
all-5830 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0417-0.0082-0.08290.094-0.10340.33660.05170.0130.0045-0.0145-0.0619-0.0221-0.11040.06810.01020.07970.0030.01870.05670.00680.012316.233311.6588.451
20.0266-0.0018-0.09050.1988-0.0620.3328-0.01320.0023-0.0160.0715-0.04180.02620.03350.00060.05490.0359-0.02120.0220.0356-0.02810.03024.7987-12.222826.0748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 701
2X-RAY DIFFRACTION2B1 - 701

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