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- PDB-8fjo: X-ray crystal structure of CYP124A1 from Mycobacterium Marinum in... -

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Basic information

Entry
Database: PDB / ID: 8fjo
TitleX-ray crystal structure of CYP124A1 from Mycobacterium Marinum in complex with farnesyl acetate
ComponentsCytochrome P450 124A1, Cyp124A1
KeywordsOXIDOREDUCTASE/SUBSTRATE / substrate bound / OXIDOREDUCTASE / OXIDOREDUCTASE-SUBSTRATE complex
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / AMMONIUM ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-Y7R / Cytochrome P450 124A1, Cyp124A1
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsGhith, A. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210103970 Australia
CitationJournal: Arch.Biochem.Biophys. / Year: 2023
Title: The catalytic activity and structure of the lipid metabolizing CYP124 cytochrome P450 enzyme from Mycobacterium marinum.
Authors: Ghith, A. / Bruning, J.B. / Bell, S.G.
History
DepositionDec 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 124A1, Cyp124A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,03311
Polymers49,2891
Non-polymers1,74410
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.511, 71.635, 64.624
Angle α, β, γ (deg.)90.00, 109.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-841-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450 124A1, Cyp124A1


Mass: 49289.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / Gene: cyp124A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2HHT9

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Non-polymers , 7 types, 259 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-Y7R / (2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl acetate / (2E,6E)-farnesyl acetate


Mass: 264.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H28O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.15 M Ammonium sulfate, 20% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.69→46.78 Å / Num. obs: 46899 / % possible obs: 98.3 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Rrim(I) all: 0.096 / Χ2: 0.5 / Net I/σ(I): 9.4
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 69.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 1.524 / Num. measured all: 8736 / Num. unique obs: 1711 / CC1/2: 0.554 / Rpim(I) all: 0.692 / Rrim(I) all: 1.681 / Χ2: 0.35 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.18.2-3874refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→45.92 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 2285 4.87 %
Rwork0.1765 --
obs0.1782 46899 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 115 249 3676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163581
X-RAY DIFFRACTIONf_angle_d2.1784882
X-RAY DIFFRACTIONf_dihedral_angle_d24.09510
X-RAY DIFFRACTIONf_chiral_restr0.095512
X-RAY DIFFRACTIONf_plane_restr0.016642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.730.34831150.34192803X-RAY DIFFRACTION100
1.73-1.770.33991260.29282783X-RAY DIFFRACTION100
1.77-1.810.3341520.26922759X-RAY DIFFRACTION100
1.81-1.860.27731370.24692777X-RAY DIFFRACTION100
1.86-1.910.271440.22712765X-RAY DIFFRACTION100
1.91-1.980.2471300.19972792X-RAY DIFFRACTION100
1.98-2.050.23921240.18032796X-RAY DIFFRACTION100
2.05-2.130.20491490.1712752X-RAY DIFFRACTION100
2.13-2.230.1921330.15772826X-RAY DIFFRACTION100
2.23-2.340.25011380.16152775X-RAY DIFFRACTION100
2.34-2.490.18881710.16662767X-RAY DIFFRACTION100
2.49-2.680.18661770.16572756X-RAY DIFFRACTION100
2.68-2.950.18971450.17032790X-RAY DIFFRACTION100
2.95-3.380.21261570.17132789X-RAY DIFFRACTION100
3.38-4.260.18511530.15282798X-RAY DIFFRACTION100
4.26-45.920.20211340.16682886X-RAY DIFFRACTION100

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