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- PDB-9jip: CYP105A1 R84A complexed with flufenamic acid (FLF) -

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Basic information

Entry
Database: PDB / ID: 9jip
TitleCYP105A1 R84A complexed with flufenamic acid (FLF)
ComponentsVitamin D3 dihydroxylase
KeywordsOXIDOREDUCTASE / P450 / CYP105A1 / nonsteroidal anti-inflammatory drugs / flufenamic acid (FLF) / 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-[[3-(TRIFLUOROMETHYL)PHENYL]AMINO] BENZOIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Vitamin D3 dihydroxylase
Similarity search - Component
Biological speciesStreptomyces griseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsMikami, B. / Takita, T. / Sakaki, T. / Yasuda, K. / Wada, M. / Yasukawa, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K05441 Japan
Japan Society for the Promotion of Science (JSPS)25292062 Japan
Citation
Journal: Biochemistry / Year: 2025
Title: Structure-Function Analysis of Streptomyces griseolus CYP105A1 in the Metabolism of Nonsteroidal Anti-inflammatory Drugs.
Authors: Takita, T. / Wada, M. / Yamagata, M. / Kamata, S. / Mizutani, K. / Yogo, Y. / Hamada, M. / Yasuda, K. / Mikami, B. / Sakaki, T. / Yasukawa, K.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 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)46,32410
Polymers44,9921
Non-polymers1,3329
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.444, 53.723, 140.625
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-FLF / 2-[[3-(TRIFLUOROMETHYL)PHENYL]AMINO] BENZOIC ACID / FLUFENAMIC ACID


Mass: 281.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10F3NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.24 Å3/Da / Density % sol: 45.22 % / Description: red rectangle plate
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 12-20% PEG4000, 10% MPD, 0.2 M NaCl, and 0.1 M Bis-Tris (pH 6.1) flufenamic acid (FLF) was introduced by 3 times soaking the crystal to the mother liqure containing 6 mM FLF.

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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: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 45929 / % possible obs: 98.6 % / Redundancy: 6.43 % / Biso Wilson estimate: 30.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.041 / Net I/σ(I): 23.37
Reflection shellResolution: 1.68→1.78 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.42 / Num. unique obs: 7218 / CC1/2: 0.837 / Rrim(I) all: 0.675 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→42.69 Å / SU ML: 0.2493 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2569 2297 5 %
Rwork0.2159 43631 -
obs0.218 45928 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.92 Å2
Refinement stepCycle: LAST / Resolution: 1.68→42.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3113 0 91 198 3402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713359
X-RAY DIFFRACTIONf_angle_d0.93034600
X-RAY DIFFRACTIONf_chiral_restr0.0547517
X-RAY DIFFRACTIONf_plane_restr0.0083610
X-RAY DIFFRACTIONf_dihedral_angle_d15.99251249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.710.35141390.33572632X-RAY DIFFRACTION97.09
1.71-1.750.32991390.29892652X-RAY DIFFRACTION97.18
1.75-1.80.32741410.28962679X-RAY DIFFRACTION98.74
1.8-1.840.35111420.28462690X-RAY DIFFRACTION98.71
1.84-1.90.33761410.27822681X-RAY DIFFRACTION98.05
1.9-1.960.35731400.28422668X-RAY DIFFRACTION98.25
1.96-2.030.31131430.27892713X-RAY DIFFRACTION98.62
2.03-2.110.29861420.2632694X-RAY DIFFRACTION98.78
2.11-2.210.32591440.25522727X-RAY DIFFRACTION99
2.21-2.320.32731430.26082725X-RAY DIFFRACTION99.17
2.32-2.470.29951440.24952743X-RAY DIFFRACTION99.35
2.47-2.660.30291450.23912742X-RAY DIFFRACTION98.97
2.66-2.930.2821450.22962761X-RAY DIFFRACTION99.11
2.93-3.350.2291460.20862783X-RAY DIFFRACTION99.22
3.35-4.220.19741480.17272803X-RAY DIFFRACTION99.13
4.22-42.690.2151550.17542938X-RAY DIFFRACTION98.72

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