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- PDB-5x7e: Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 ... -

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Basic information

Entry
Database: PDB / ID: 5x7e
TitleCrystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant) in complex with 1,25-dihydroxyvitamin D2
ComponentsVitamin D3 dihydroxylase
KeywordsOXIDOREDUCTASE / METAL-BINDING / MONOOXYGENASE
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 / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7ZU / PROTOPORPHYRIN IX CONTAINING FE / Vitamin D3 dihydroxylase
Similarity search - Component
Biological speciesStreptomyces griseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
Model detailsCYP105A1 in complex with active form of vitamin D2
AuthorsHayashi, K. / Yasuda, K. / Shiro, Y. / Sugimoto, H. / Sakaki, T.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Production of an active form of vitamin D2 by genetically engineered CYP105A1
Authors: Yasuda, K. / Yogo, Y. / Sugimoto, H. / Mano, H. / Takita, T. / Ohta, M. / Kamakura, M. / Ikushiro, S. / Yasukawa, K. / Shiro, Y. / Sakaki, T.
History
DepositionFeb 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)46,0373
Polymers44,9921
Non-polymers1,0452
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-24 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.409, 53.360, 139.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Plasmid: pKK223-3 / 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-7ZU / (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(E,2R,5S)-5,6-dimethyl-6-oxidanyl-hept-3-en-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydr o-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol / 1,25-dihydroxyvitamin D2


Mass: 428.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H44O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.27 % / Mosaicity: 0.59 °
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 6.8 / Details: 26% PEGMME 20000, 0.2 M NaCl, 0.1 M BisTris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 10, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 30958 / % possible obs: 98 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 12
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.3 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZBZ

2zbz


Resolution: 1.9→17.53 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.426 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1563 5.1 %RANDOM
Rwork0.186 ---
obs0.188 29341 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.26 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 74 294 3458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193246
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6792.0254447
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5735405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35723.472144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54315504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0231530
X-RAY DIFFRACTIONr_chiral_restr0.1140.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212512
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 103 -
Rwork0.206 1877 -
obs--87.3 %

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