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- PDB-7q84: Crystal structure of human peroxisomal acyl-Co-A oxidase 1a, apo-form -

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Basic information

Entry
Database: PDB / ID: 7q84
TitleCrystal structure of human peroxisomal acyl-Co-A oxidase 1a, apo-form
ComponentsIsoform 2 of Peroxisomal acyl-coenzyme A oxidase 1
KeywordsOXIDOREDUCTASE / acyl-Co-A oxidase / peroxisomal enzyme
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSonani, R.R. / Blat, A. / Dubin, G.
Funding support2items
OrganizationGrant numberCountry
Polish National Science Centre2017/26/M/NZ1/00797
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)152,81118
Polymers151,5072
Non-polymers1,30316
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14950 Å2
ΔGint-3 kcal/mol
Surface area45920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.871, 133.222, 139.564
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 508 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.73 Å3/Da / Density % sol: 54.96 %
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)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→48.18 Å / Num. obs: 110023 / % possible obs: 99.03 % / Redundancy: 13.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.026 / Rrim(I) all: 0.096 / Net I/σ(I): 17.38
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 1.319 / Num. unique obs: 10875 / CC1/2: 0.86 / CC star: 0.962 / Rpim(I) all: 0.358 / Rrim(I) all: 1.367 / % possible all: 99.35

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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: 1is2

1is2


Resolution: 2→48.23 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 10.326 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 5573 5.1 %RANDOM
Rwork0.1835 ---
obs0.1854 104443 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 153.54 Å2 / Biso mean: 47.835 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-6.06 Å20 Å2-0 Å2
2---3.18 Å20 Å2
3----2.88 Å2
Refinement stepCycle: final / Resolution: 2→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9979 0 85 492 10556
Biso mean--60.54 47.59 -
Num. residues----1253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01310284
X-RAY DIFFRACTIONr_bond_other_d0.0040.0179804
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.64613877
X-RAY DIFFRACTIONr_angle_other_deg1.4821.57622573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86951246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1322.134539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.067151784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2341566
X-RAY DIFFRACTIONr_chiral_restr0.0940.21324
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211478
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022366
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 423 -
Rwork0.323 7623 -
all-8046 -
obs--99.22 %
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)
10.0770.04720.15290.13710.10840.30860.03720.0046-0.0007-0.0322-0.03210.02680.06810.0047-0.00510.06250.0137-0.00790.0138-0.00920.0138-17.4645-13.91768.1983
20.0183-0.0130.05750.28280.16630.339-0.02090.01220.01080.0570.0064-0.025-0.02410.05080.01450.0258-0.0102-0.01610.01090.01170.0273-3.78277.267225.572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 709
2X-RAY DIFFRACTION2B1 - 707

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