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- PDB-9ule: Crystal structure of CYP105A1 R84A complexed with diclofenac (DIF... -

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Basic information

Entry
Database: PDB / ID: 9ule
TitleCrystal structure of CYP105A1 R84A complexed with diclofenac (DIF) at room temperature
ComponentsVitamin D3 dihydroxylase
KeywordsOXIDOREDUCTASE / P450 / CYP105A1 / nonsteroidal anti-inflammatory drugs / diclofenac / flufenamic acid / R84A
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
2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Vitamin D3 dihydroxylase
Similarity search - Component
Biological speciesStreptomyces griseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsMikami, B. / Takita, T. / Yoneda, S. / Yasuda, K. / Sakaki, T. / Yasukawa, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K05441 Japan
CitationJournal: to be published
Title: Complex formation of Streptomyces griseolus CYP105A1 with statins by room-temperature crystal data collection
Authors: Takita, T. / Yoneda, S. / Yasuda, K. / Mizutani, K. / Yasukawa, K. / Mikami, B. / Sakaki, T.
History
DepositionApr 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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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)45,9043
Polymers44,9921
Non-polymers9132
Water3,819212
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)53.859, 54.039, 144.700
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
Source: (gene. exp.) Streptomyces griseolus (bacteria) / Gene: cyp105A1, suaC / 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
#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-DIF / 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID / DICLOFENAC


Mass: 296.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11Cl2NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory, medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.34 Å3/Da / Density % sol: 47.44 % / Description: Red lectangle crystal with 0.4 X 0.4 x 0.2 mm.
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 12-18% PEG4000, 10% MPD, 0.2 M NaCl and 0.1 M Bis-Tris buffer with protein concentration of 5 mg/ml. The crystal was soaked 3 times each for 10 min in the mother liquare containg 10 mM ...Details: 12-18% PEG4000, 10% MPD, 0.2 M NaCl and 0.1 M Bis-Tris buffer with protein concentration of 5 mg/ml. The crystal was soaked 3 times each for 10 min in the mother liquare containg 10 mM Diclofenac. The soaked crystal was placed into a glass capillary and sealed with dental wax after the solution was added to one end of the capillary.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 35228 / % possible obs: 96.3 % / Redundancy: 5.16 % / Biso Wilson estimate: 26.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.063 / Net I/σ(I): 18.81
Reflection shellResolution: 1.86→1.97 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 3.81 / Num. unique obs: 5519 / CC1/2: 0.884 / Rrim(I) all: 0.573

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→36.17 Å / SU ML: 0.1903 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2076 1761 5 %
Rwork0.1596 33465 -
obs0.1619 35226 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.42 Å2
Refinement stepCycle: LAST / Resolution: 1.86→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3088 0 62 212 3362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663380
X-RAY DIFFRACTIONf_angle_d0.92394648
X-RAY DIFFRACTIONf_chiral_restr0.0533523
X-RAY DIFFRACTIONf_plane_restr0.009621
X-RAY DIFFRACTIONf_dihedral_angle_d15.37571284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.910.29611300.24172464X-RAY DIFFRACTION94.74
1.91-1.960.25251320.20582539X-RAY DIFFRACTION96.5
1.96-2.020.25211350.18752552X-RAY DIFFRACTION97.36
2.02-2.10.2231360.17352585X-RAY DIFFRACTION97.91
2.1-2.180.22231360.16942592X-RAY DIFFRACTION97.92
2.18-2.280.1991360.15812571X-RAY DIFFRACTION97.69
2.28-2.40.21861370.16362604X-RAY DIFFRACTION98.1
2.4-2.550.19431370.16642618X-RAY DIFFRACTION97.59
2.55-2.750.22621370.17342594X-RAY DIFFRACTION97.68
2.75-3.020.21741370.17892603X-RAY DIFFRACTION96.68
3.02-3.460.21891350.16632566X-RAY DIFFRACTION95.58
3.46-4.360.19021350.13422556X-RAY DIFFRACTION93.76
4.36-36.170.18041380.13792621X-RAY DIFFRACTION91

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