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- PDB-9kw4: Crystal structure of CYP105A1 R84A and miconazole complex -

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Basic information

Entry
Database: PDB / ID: 9kw4
TitleCrystal structure of CYP105A1 R84A and miconazole complex
ComponentsVitamin D3 dihydroxylase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Inhibitor / Heme / EI complex
Function / homology
Function and homology information


vitamin D 1,25-hydroxylase / vitamin D3 metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
: / PROTOPORPHYRIN IX CONTAINING FE / Vitamin D3 dihydroxylase
Similarity search - Component
Biological speciesStreptomyces griseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHirano, Y. / Yoneda, S. / Yasuda, K. / Takimoto-Kamimura, M. / Sakaki, T. / Tamada, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JPMXS0120330644 Japan
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Cooperative inhibition in cytochrome P450 between a substrate and an apparent noncompetitive inhibitor.
Authors: Hirano, Y. / Yoneda, S. / Yasuda, K. / Kurita, N. / Kawagoe, F. / Mikami, B. / Takita, T. / Yasukawa, K. / Ikushiro, S. / Takimoto-Kamimura, M. / Kittaka, A. / Sakaki, T. / Tamada, T.
History
DepositionDec 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitamin D3 dihydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1474
Polymers44,9921
Non-polymers1,1553
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-24 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.286, 53.481, 140.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Vitamin D3 dihydroxylase / CYP105A1 / Cytochrome P450-CVA1 / Cytochrome P450-SU1 / Vitamin D3 hydroxylase / VD3 hydroxylase


Mass: 44991.742 Da / Num. of mol.: 1 / Mutation: R84A
Source method: isolated from a genetically manipulated source
Details: 6xHis-tag fused to the C-terminus / Source: (gene. exp.) Streptomyces griseolus (bacteria) / Gene: cyp105A1, suaC / Production host: Escherichia coli (E. coli)
References: UniProt: P18326, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one ...References: UniProt: P18326, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen into the other donor
#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-A1L6X / 1-[(2S)-2-(2,4-dichlorophenyl)-2-[(2,4-dichlorophenyl)methoxy]ethyl]imidazole / miconazole


Mass: 416.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14Cl4N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24% (w/v) PEG 2000 MME, 50mM Bis-Tris pH 6.5, 0.2M NaCl

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2022
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→42.5 Å / Num. obs: 37286 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.084 / Net I/σ(I): 14
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2156 / CC1/2: 0.914 / Rrim(I) all: 0.532 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→42.5 Å / SU ML: 0.2126 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7371
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228 1767 4.75 %
Rwork0.1838 35424 -
obs0.1859 37191 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3081 0 76 294 3451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693393
X-RAY DIFFRACTIONf_angle_d0.854652
X-RAY DIFFRACTIONf_chiral_restr0.0518514
X-RAY DIFFRACTIONf_plane_restr0.0051619
X-RAY DIFFRACTIONf_dihedral_angle_d14.60351259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.2991510.22262619X-RAY DIFFRACTION99.07
1.85-1.90.27861370.21642679X-RAY DIFFRACTION99.82
1.9-1.960.26041260.2072700X-RAY DIFFRACTION99.93
1.96-2.030.29461340.20422679X-RAY DIFFRACTION99.89
2.03-2.120.24721160.19172707X-RAY DIFFRACTION99.96
2.12-2.210.23631540.18442686X-RAY DIFFRACTION99.79
2.21-2.330.24441490.18482691X-RAY DIFFRACTION100
2.33-2.480.26121320.18732715X-RAY DIFFRACTION99.96
2.48-2.670.24631360.19252743X-RAY DIFFRACTION99.93
2.67-2.930.27071090.2042738X-RAY DIFFRACTION99.96
2.93-3.360.2281300.19752764X-RAY DIFFRACTION100
3.36-4.230.19841410.1642778X-RAY DIFFRACTION100
4.23-42.50.1711520.15782925X-RAY DIFFRACTION99.81

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