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- PDB-8fkb: X-ray crystal structure of CYP124A1 from Mycobacterium Marinum bo... -

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Basic information

Entry
Database: PDB / ID: 8fkb
TitleX-ray crystal structure of CYP124A1 from Mycobacterium Marinum bound to Farnesol
ComponentsCytochrome P450 124A1
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
(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cytochrome P450 124A1, Cyp124A1
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,31212
Polymers48,4611
Non-polymers1,85211
Water5,711317
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.456, 72.425, 65.505
Angle α, β, γ (deg.)90.00, 109.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450 124A1 / Cyp124A1


Mass: 48460.605 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 , 6 types, 328 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-FOF / (2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol / trans,trans-Farnesol


Mass: 222.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.15M ammonium Sulfate, 20% PEG 3350

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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: 1.42→47.02 Å / Num. obs: 80390 / % possible obs: 97.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Χ2: 0.49 / Net I/σ(I): 9.7 / Num. measured all: 549105
Reflection shellResolution: 1.42→1.44 Å / % possible obs: 78.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.725 / Num. measured all: 20050 / Num. unique obs: 3264 / CC1/2: 0.891 / Rpim(I) all: 0.306 / Rrim(I) all: 0.789 / Χ2: 0.26 / Net I/σ(I) obs: 1.2

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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: 1.42→47.02 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2001 1995 2.48 %
Rwork0.1826 --
obs0.1831 80304 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 62 317 3758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113577
X-RAY DIFFRACTIONf_angle_d1.3354871
X-RAY DIFFRACTIONf_dihedral_angle_d28.117512
X-RAY DIFFRACTIONf_chiral_restr0.091511
X-RAY DIFFRACTIONf_plane_restr0.01639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.450.45681130.41634863X-RAY DIFFRACTION85
1.45-1.490.38061560.33435533X-RAY DIFFRACTION98
1.49-1.540.32891390.29555570X-RAY DIFFRACTION98
1.54-1.580.26261320.27475576X-RAY DIFFRACTION98
1.58-1.640.28821490.23075575X-RAY DIFFRACTION98
1.64-1.710.24811440.20135650X-RAY DIFFRACTION98
1.71-1.790.2261530.18035620X-RAY DIFFRACTION99
1.79-1.880.18661330.17485633X-RAY DIFFRACTION99
1.88-20.19181470.17615666X-RAY DIFFRACTION99
2-2.150.19391420.16325650X-RAY DIFFRACTION99
2.15-2.370.15741460.15625674X-RAY DIFFRACTION99
2.37-2.710.16581460.16415722X-RAY DIFFRACTION99
2.71-3.410.19071450.17815754X-RAY DIFFRACTION100
3.41-47.020.18861500.16675823X-RAY DIFFRACTION100

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