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- PDB-8flo: X-ray crystal structure of substrate free CYP124A1 from Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 8flo
TitleX-ray crystal structure of substrate free CYP124A1 from Mycobacterium Marinum
ComponentsCytochrome P450 124A1
KeywordsOXIDOREDUCTASE / substrate free
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Cytochrome P450 124A1, Cyp124A1
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 22, 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)50,3927
Polymers49,2891
Non-polymers1,1036
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.715, 72.827, 65.343
Angle α, β, γ (deg.)90.00, 109.38, 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: 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 , 5 types, 231 molecules

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


Mass: 616.487 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.26 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: 0.95 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.71→47.07 Å / Num. obs: 47090 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.093 / Rrim(I) all: 0.246 / Χ2: 0.85 / Net I/σ(I): 4.9 / Num. measured all: 326844
Reflection shellResolution: 1.71→1.74 Å / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 7.116 / Num. measured all: 16447 / Num. unique obs: 2464 / CC1/2: 0.463 / Rpim(I) all: 3.1 / Rrim(I) all: 7.801 / Χ2: 0.71 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→45.03 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 2267 4.89 %
Rwork0.2037 --
obs0.2059 46394 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 76 225 3611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153478
X-RAY DIFFRACTIONf_angle_d1.9324745
X-RAY DIFFRACTIONf_dihedral_angle_d18.767471
X-RAY DIFFRACTIONf_chiral_restr0.08504
X-RAY DIFFRACTIONf_plane_restr0.011621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.41461030.45932621X-RAY DIFFRACTION94
1.75-1.790.48391200.40822666X-RAY DIFFRACTION95
1.79-1.830.44271450.37422702X-RAY DIFFRACTION97
1.83-1.880.39591420.34432696X-RAY DIFFRACTION97
1.88-1.940.37041420.31972726X-RAY DIFFRACTION98
1.94-20.3491290.29552760X-RAY DIFFRACTION98
2-2.070.30581280.24982814X-RAY DIFFRACTION99
2.07-2.160.26411510.22472725X-RAY DIFFRACTION100
2.16-2.250.25491240.19952835X-RAY DIFFRACTION99
2.25-2.370.30821450.1982744X-RAY DIFFRACTION99
2.37-2.520.22791690.19232769X-RAY DIFFRACTION99
2.52-2.720.25011770.19332758X-RAY DIFFRACTION100
2.72-2.990.25541470.19692812X-RAY DIFFRACTION100
2.99-3.420.24651580.19482794X-RAY DIFFRACTION100
3.42-4.310.19041530.16652809X-RAY DIFFRACTION100
4.31-45.030.20671340.16172896X-RAY DIFFRACTION100

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