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- PDB-9fxq: Ancestral Prenylcysteine Oxidase 1 (PCYOX1) -

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Basic information

Entry
Database: PDB / ID: 9fxq
TitleAncestral Prenylcysteine Oxidase 1 (PCYOX1)
ComponentsAncestral Prenylcysteine Oxidase 1 (PCYOX1)
KeywordsFLAVOPROTEIN / Oxidoreductase / Oxidative Metabolism / Protein Prenylation / Ancestral Enzyme
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesMammalia (mammals)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBarone, M. / Mattevi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education2020CW39SJ Italy
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Evolution, structure, and drug-metabolizing activity of mammalian prenylcysteine oxidases.
Authors: Barone, M. / Pizzorni, L. / Fraaije, M.W. / Mascotti, M.L. / Mattevi, A.
History
DepositionJul 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ancestral Prenylcysteine Oxidase 1 (PCYOX1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3413
Polymers53,9401
Non-polymers1,4002
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-8 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.659, 172.659, 172.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Ancestral Prenylcysteine Oxidase 1 (PCYOX1)


Mass: 53940.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalia (mammals) / Production host: Escherichia coli (E. coli) / References: EC: 1.8.3.5
#2: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY
Has protein modificationN

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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: 3.89 Å3/Da / Density % sol: 68.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0 M Ammonium Sulfate, 0.1 M HEPES, 5% Isopropanol, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 3.1→172.77 Å / Num. obs: 16624 / % possible obs: 100 % / Redundancy: 57.6 % / CC1/2: 1 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.03 / Rrim(I) all: 0.19 / Net I/σ(I): 15.3
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 26.7 % / Mean I/σ(I) obs: 1.56 / Num. unique obs: 2936 / CC1/2: 0.34 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimless0.7.13data scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→122.39 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.918 / SU B: 63.366 / SU ML: 0.431 / Cross valid method: THROUGHOUT / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27546 1646 10 %RANDOM
Rwork0.22528 ---
obs0.23015 14894 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 150.297 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3.1→122.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 75 0 3729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123852
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163584
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.825232
X-RAY DIFFRACTIONr_angle_other_deg0.6311.7458254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8095462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.764517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.09410630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02900
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.43210.6241857
X-RAY DIFFRACTIONr_mcbond_other10.4210.6251857
X-RAY DIFFRACTIONr_mcangle_it15.5719.0652316
X-RAY DIFFRACTIONr_mcangle_other15.56719.0692317
X-RAY DIFFRACTIONr_scbond_it12.25111.3431995
X-RAY DIFFRACTIONr_scbond_other12.18811.3451992
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other18.51620.5042917
X-RAY DIFFRACTIONr_long_range_B_refined27.407277.52273395
X-RAY DIFFRACTIONr_long_range_B_other27.407277.52273396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.178 Å
RfactorNum. reflection% reflection
Rfree0.503 98 -
Rwork0.45 1086 -
obs--99.58 %
Refinement TLS params.Method: refined / Origin x: -24.1805 Å / Origin y: 19.7459 Å / Origin z: -21.2617 Å
111213212223313233
T0.3613 Å2-0.2768 Å20.0085 Å2-0.3369 Å2-0.0079 Å2--0.0399 Å2
L2.2862 °2-0.231 °20.2279 °2-4.091 °2-1.3779 °2--2.5618 °2
S-0.0518 Å °0.1181 Å °0.1202 Å °0.5924 Å °-0.13 Å °-0.2527 Å °-0.4839 Å °0.468 Å °0.1818 Å °

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