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- PDB-3cv8: Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 ... -

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Basic information

Entry
Database: PDB / ID: 3cv8
TitleCrystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84F mutant)
ComponentsCytochrome P450-SU1
KeywordsOXIDOREDUCTASE / P450 / BETA PRISM / HEME / IRON / 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Vitamin D3 dihydroxylase
Similarity search - Component
Biological speciesStreptomyces griseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHayashi, K. / Sugimoto, H. / Shinkyo, R. / Yamada, M. / Ikeda, S. / Ikushiro, S. / Kamakura, M. / Shiro, Y. / Sakaki, T.
Citation
Journal: Biochemistry / Year: 2008
Title: Structure-based design of a highly active vitamin D hydroxylase from Streptomyces griseolus CYP105A1
Authors: Hayashi, K. / Sugimoto, H. / Shinkyo, R. / Yamada, M. / Ikeda, S. / Ikushiro, S. / Kamakura, M. / Shiro, Y. / Sakaki, T.
#1: Journal: Biochemistry / Year: 2008
Title: Crystal Structure of CYP105A1 (P450SU-1) in Complex with 1alpha,25-Dihydroxyvitamin D3
Authors: Sugimoto, H. / Shinkyo, R. / Hayashi, K. / Yoneda, S. / Yamada, M. / Kamakura, M. / Ikushiro, S. / Shiro, Y. / Sakaki, T.
History
DepositionApr 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450-SU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6842
Polymers45,0681
Non-polymers6161
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.500, 53.384, 138.970
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 Cytochrome P450-SU1 / P450-CVA1 / CYP105A1


Mass: 45067.836 Da / Num. of mol.: 1 / Mutation: R84F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseolus (bacteria) / Strain: ATCC 11796 / Gene: CYP105A1 / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P18326, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS A CONFLICT BETWEEN THE SEQUENCES GIVEN IN THE DEPOSITION AND THE DATABASE. ACCORDING TO ...THERE IS A CONFLICT BETWEEN THE SEQUENCES GIVEN IN THE DEPOSITION AND THE DATABASE. ACCORDING TO THE DEPOSITOR, THE 308TH RESIDUE IS GLN AND IT OCCURS NATURALLY AS VARIANT IN STREPTOMYCES GRISEOLUS.

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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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 16% PEGMME 2000, 10% MPD, 0.1M Bis-tris, 0.2M sodium chloride, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 18, 2007 / Details: mirrors
RadiationMonochromator: Si (1 1 1) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 27037 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 23.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 8.3 / Num. unique all: 2617 / Rsym value: 0.191 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZBZ

2zbz


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.963 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22992 1378 5.1 %RANDOM
Rwork0.18112 ---
obs0.18356 25633 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.306 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---1.05 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 43 346 3496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223223
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2712.0124412
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4735407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88723.333147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79615508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9941531
X-RAY DIFFRACTIONr_chiral_restr0.0890.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022492
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21614
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.22230
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2336
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.711.52073
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18923257
X-RAY DIFFRACTIONr_scbond_it1.84931276
X-RAY DIFFRACTIONr_scangle_it2.9724.51150
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 88 -
Rwork0.207 1820 -
obs--97.25 %

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