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- PDB-9njw: Structure of ancestral-reconstructed cytochrome P450 11A1 (CYP11A... -

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Basic information

Entry
Database: PDB / ID: 9njw
TitleStructure of ancestral-reconstructed cytochrome P450 11A1 (CYP11A1) in complex with cholesterol
ComponentsCytochrome P450, CYP11A1
KeywordsOXIDOREDUCTASE / Cytochrome P450 / steroidogenesis / cholesterol / evolution
Function / homologyCHOLESTEROL / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChagas, B.C. / Wang, P.C. / Brixius-Anderko, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Inorg.Biochem. / Year: 2025
Title: How evolution shaped the structure of steroidogenic cytochrome P450 11A.
Authors: Chagas, B.C.A. / Brixius, B. / Wang, P.C. / Pirhadi, S. / Aziz, O. / Koes, D.R. / Gillam, E.M.J. / Bernhardt, R. / Brixius-Anderko, S.
History
DepositionFeb 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450, CYP11A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3543
Polymers56,3511
Non-polymers1,0032
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.894, 155.894, 155.894
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2

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Components

#1: Protein Cytochrome P450, CYP11A1


Mass: 56350.805 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.8 Å3/Da / Density % sol: 56.09 % / Description: Cubic
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Sodium chloride, 0.1 M Bis-tris propane pH 9.0, 20.5% w/v Polyethylene glycol 1,500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.39→38.97 Å / Num. obs: 25022 / % possible obs: 99.7 % / Redundancy: 40.7 % / Biso Wilson estimate: 65.06 Å2 / CC1/2: 1 / Rpim(I) all: 0.019 / Net I/σ(I): 22.8
Reflection shellResolution: 2.39→2.52 Å / Redundancy: 38.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3562 / CC1/2: 0.474 / Rpim(I) all: 0.611 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoXDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.97 Å / SU ML: 0.3843 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2596 2005 8.1 %
Rwork0.227 22753 -
obs0.2297 24758 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 0 71 9 3871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313965
X-RAY DIFFRACTIONf_angle_d0.51555391
X-RAY DIFFRACTIONf_chiral_restr0.0387578
X-RAY DIFFRACTIONf_plane_restr0.0035683
X-RAY DIFFRACTIONf_dihedral_angle_d13.52441505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.39511360.33451526X-RAY DIFFRACTION94.16
2.46-2.520.40961410.32161585X-RAY DIFFRACTION99.94
2.52-2.60.32061430.33211653X-RAY DIFFRACTION99.89
2.6-2.680.37131420.32571610X-RAY DIFFRACTION99.89
2.68-2.780.35811420.30761605X-RAY DIFFRACTION99.94
2.78-2.890.39211430.30561626X-RAY DIFFRACTION99.94
2.89-3.020.35221360.3121606X-RAY DIFFRACTION99.89
3.02-3.180.34111440.30431631X-RAY DIFFRACTION100
3.18-3.380.36971460.28141639X-RAY DIFFRACTION100
3.38-3.640.27671380.24721635X-RAY DIFFRACTION100
3.64-40.2331480.22091629X-RAY DIFFRACTION99.94
4-4.580.22931460.19631648X-RAY DIFFRACTION100
4.59-5.750.22281490.18971648X-RAY DIFFRACTION100
5.77-38.970.19461510.17141712X-RAY DIFFRACTION99.79

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