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- PDB-8vxi: The crystal structure of sitosterol-bound CYP125MRCA -

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Basic information

Entry
Database: PDB / ID: 8vxi
TitleThe crystal structure of sitosterol-bound CYP125MRCA
ComponentsCYP125MRCA
KeywordsLIPID BINDING PROTEIN / P450 / Cytochrome / Heme / Sitosterol / Phytosterols / CYP125 / Ancestor
Function / homology: / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.057 Å
AuthorsDoherty, D.Z. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210103970 Australia
CitationJournal: Chem Sci / Year: 2025
Title: Evolutionary insights into the selectivity of sterol oxidising cytochrome P450 enzymes based on ancestral sequence reconstruction.
Authors: Doherty, D.Z. / De Voss, J.J. / Bruning, J.B. / Bell, S.G.
History
DepositionFeb 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYP125MRCA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1483
Polymers48,1171
Non-polymers1,0312
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.957, 118.880, 94.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CYP125MRCA


Mass: 48116.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-A1LXL / Beta-Sitosterol / (3S,8S,9S,10R,13R,14S,17R)-17-[(2R,5R)-5-ethyl-6-methylheptan-2-yl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol


Mass: 414.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H50O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 20% PEG4000, 20% Isopropanol, 0.1M Sodium Citrate Tribasic Dihydrate
PH range: 5.2 - 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953731894493 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731894493 Å / Relative weight: 1
ReflectionResolution: 2.057→47.38 Å / Num. obs: 25931 / % possible obs: 99.8 % / Redundancy: 13.5 % / CC1/2: 0.998 / Net I/σ(I): 9.8
Reflection shellResolution: 2.06→2.11 Å / Num. unique obs: 1950 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.057→47.38 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2153 2003 7.73 %
Rwork0.1738 --
obs0.177 25901 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.057→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 73 273 3525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033351
X-RAY DIFFRACTIONf_angle_d1.2624563
X-RAY DIFFRACTIONf_dihedral_angle_d10.6862024
X-RAY DIFFRACTIONf_chiral_restr0.141479
X-RAY DIFFRACTIONf_plane_restr0.006604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.057-2.10850.30291270.25331655X-RAY DIFFRACTION97
2.1085-2.16550.24641460.22921668X-RAY DIFFRACTION100
2.1655-2.22920.25381400.21061687X-RAY DIFFRACTION100
2.2292-2.30120.21661430.19241700X-RAY DIFFRACTION100
2.3012-2.38340.24391390.18751681X-RAY DIFFRACTION100
2.3834-2.47880.25241390.18821701X-RAY DIFFRACTION100
2.4788-2.59160.24991530.18691693X-RAY DIFFRACTION100
2.5916-2.72830.23171370.1941695X-RAY DIFFRACTION100
2.7283-2.89920.20161430.18881716X-RAY DIFFRACTION100
2.8992-3.1230.21561440.18611687X-RAY DIFFRACTION100
3.123-3.43720.24571470.17551722X-RAY DIFFRACTION100
3.4372-3.93430.21351460.15791720X-RAY DIFFRACTION100
3.9343-4.9560.17211480.13581755X-RAY DIFFRACTION100
4.956-47.380.18871510.15961818X-RAY DIFFRACTION100

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