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- PDB-3cv9: Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 ... -

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Basic information

Entry
Database: PDB / ID: 3cv9
TitleCrystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R73A/R84A mutant) in complex with 1alpha,25-dihydroxyvitamin D3
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 / Chem-VDX / Vitamin D3 dihydroxylase
Similarity search - Component
Biological speciesStreptomyces griseolus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)45,9393
Polymers44,9061
Non-polymers1,0332
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.315, 53.659, 140.605
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: 44905.629 Da / Num. of mol.: 1 / Mutation: R73A, R84A
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: Chemical ChemComp-VDX / 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL / 1,25 DIHYDROXY VITAMIN D3


Mass: 416.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 26% PEGMME 2000, 0.1M Bis-tris, 0.2M sodium chlorife, pH 6.2, 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 28, 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: 1.7→20 Å / Num. all: 45139 / Num. obs: 45139 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 21.6 Å2 / Rsym value: 0.04 / Net I/σ(I): 28.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 3913 / Rsym value: 0.337 / % possible all: 87.1

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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: 1.7→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.693 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25347 2266 5.1 %RANDOM
Rwork0.19907 ---
obs0.20177 42422 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.075 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---1.45 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 73 463 3686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223309
X-RAY DIFFRACTIONr_angle_refined_deg1.5542.0194546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62923.529153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30415519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2791531
X-RAY DIFFRACTIONr_chiral_restr0.1080.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022585
X-RAY DIFFRACTIONr_nbd_refined0.2120.21736
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2357
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.235
X-RAY DIFFRACTIONr_mcbond_it0.8491.52101
X-RAY DIFFRACTIONr_mcangle_it1.31623309
X-RAY DIFFRACTIONr_scbond_it2.09431354
X-RAY DIFFRACTIONr_scangle_it2.9944.51225
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 142 -
Rwork0.259 2722 -
obs--87.45 %

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