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

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Basic information

Entry
Database: PDB / ID: 9onh
TitleStructure of ancestral-reconstructed cytochrome P450 11A1 (CYP11A1) in complex with desmosterol
ComponentsAncestral Cytochrome P450 11A1 (CYP11A1)
KeywordsOXIDOREDUCTASE / Cytochrome P450 / steroidogenesis / evolution
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / desmosterol
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAlves Chagas, B.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
DepositionMay 15, 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: Ancestral Cytochrome P450 11A1 (CYP11A1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3523
Polymers56,3511
Non-polymers1,0012
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.034, 156.034, 156.034
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 Ancestral Cytochrome P450 11A1 (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-MHQ / desmosterol


Mass: 384.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O / Feature type: SUBJECT OF INVESTIGATION
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: 2.81 Å3/Da / Density % sol: 56.21 % / 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, 25% w/v Polyethylene glycol 1,500; 40 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→39.81 Å / Num. obs: 14177 / % possible obs: 100 % / Redundancy: 41.3 % / CC1/2: 0.999 / Rpim(I) all: 0.047 / Net I/σ(I): 14.7
Reflection shellResolution: 2.9→3.06 Å / Num. unique obs: 2070 / CC1/2: 0.672 / Rpim(I) all: 0.674 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoXDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→39.01 Å / SU ML: 0.4618 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.1782
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2613 714 5.04 %
Rwork0.207 13452 -
obs0.2096 14166 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.78 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 71 0 3841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00463943
X-RAY DIFFRACTIONf_angle_d0.82985360
X-RAY DIFFRACTIONf_chiral_restr0.0539576
X-RAY DIFFRACTIONf_plane_restr0.0247678
X-RAY DIFFRACTIONf_dihedral_angle_d14.30021498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.120.41991410.29922664X-RAY DIFFRACTION99.82
3.12-3.440.31921440.25042648X-RAY DIFFRACTION99.93
3.44-3.940.3011400.23492686X-RAY DIFFRACTION99.93
3.94-4.950.24351410.18982677X-RAY DIFFRACTION100
4.96-39.010.21971480.18372777X-RAY DIFFRACTION99.93

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