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- PDB-9vl0: CYP105A1 complexed with simvastatin (cryogenic data collection) -

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Basic information

Entry
Database: PDB / ID: 9vl0
TitleCYP105A1 complexed with simvastatin (cryogenic data collection)
ComponentsVitamin D3 dihydroxylase
KeywordsOXIDOREDUCTASE / P450 / CYP105A1 / statin / simvastatin
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 / DI(HYDROXYETHYL)ETHER / Vitamin D3 dihydroxylase
Similarity search - Component
Biological speciesStreptomyces griseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTakita, T. / Yoneda, S. / Yasuda, K. / Mizutani, K. / Yasukawa, K. / Sakaki, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K05441 Japan
Japan Society for the Promotion of Science (JSPS)23K24590 Japan
Japan Society for the Promotion of Science (JSPS)21380067 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2025
Title: Room-temperature X-ray data collection enabled the structural determination of statin-bound CYP105A1.
Authors: Takita, T. / Yoneda, S. / Yasuda, K. / Mizutani, K. / Yasukawa, K. / Sakaki, T. / Mikami, B.
History
DepositionJun 24, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 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: Vitamin D3 dihydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0736
Polymers44,9921
Non-polymers1,0815
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.000, 53.202, 138.801
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

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Protein , 1 types, 1 molecules A

#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
Source: (gene. exp.) Streptomyces griseolus (bacteria) / Gene: cyp105A1, suaC / Plasmid: pKSNd1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
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

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Non-polymers , 5 types, 296 molecules

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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#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: 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.: 291 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43 % / Description: red color lectangle
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: The reservoir solution was 12-20% PEG4000, 10% MPD, 0.2 M NaCl, and 0.1 M Bis-Tris (pH 6.1). The enzyme concentration was 4-6 mg/mL. The crystal was flash-cooled in the cold nitrogen gas ...Details: The reservoir solution was 12-20% PEG4000, 10% MPD, 0.2 M NaCl, and 0.1 M Bis-Tris (pH 6.1). The enzyme concentration was 4-6 mg/mL. The crystal was flash-cooled in the cold nitrogen gas stream at 100 K without cryoprotectant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 50990 / % possible obs: 98.3 % / Redundancy: 6.97 % / Biso Wilson estimate: 20.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.045 / Net I/σ(I): 26.19
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 6.85 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 3.81 / Num. unique obs: 7979 / CC1/2: 0.907 / Rrim(I) all: 0.57 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.7 Å / SU ML: 0.1748 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: An isotropic B factors were used in the model refinement.
RfactorNum. reflection% reflection
Rfree0.2021 2549 5 %
Rwork0.1535 48435 -
obs0.1559 50984 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.15 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3110 0 74 291 3475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513360
X-RAY DIFFRACTIONf_angle_d0.79874609
X-RAY DIFFRACTIONf_chiral_restr0.048523
X-RAY DIFFRACTIONf_plane_restr0.0075608
X-RAY DIFFRACTIONf_dihedral_angle_d15.25741257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.3041330.20722525X-RAY DIFFRACTION95.2
1.63-1.670.24921390.18012643X-RAY DIFFRACTION98.17
1.67-1.70.27991390.16862634X-RAY DIFFRACTION99.68
1.7-1.740.22741400.16852660X-RAY DIFFRACTION99.08
1.74-1.790.26711400.16252669X-RAY DIFFRACTION99.05
1.79-1.840.26381390.16072642X-RAY DIFFRACTION99.32
1.84-1.890.23491410.16242671X-RAY DIFFRACTION99.89
1.89-1.950.2221410.15122682X-RAY DIFFRACTION99.54
1.95-2.020.22871400.1512667X-RAY DIFFRACTION99.65
2.02-2.10.21571410.14882677X-RAY DIFFRACTION99.75
2.1-2.20.21241430.14762713X-RAY DIFFRACTION99.86
2.2-2.310.22711420.15362706X-RAY DIFFRACTION99.93
2.31-2.460.21661420.15682689X-RAY DIFFRACTION99.93
2.46-2.650.22161440.15742730X-RAY DIFFRACTION99.97
2.65-2.910.18031420.16272713X-RAY DIFFRACTION99.58
2.91-3.340.20751440.15682734X-RAY DIFFRACTION99.58
3.34-4.20.16341460.13752776X-RAY DIFFRACTION99.73
4.2-34.70.16591530.14962904X-RAY DIFFRACTION99.19

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