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- PDB-2zbz: Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 ... -

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Basic information

Entry
Database: PDB / ID: 2zbz
TitleCrystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant) in complex with 1,25-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: 1.9 Å
AuthorsSugimoto, H. / Shinkyo, R. / Hayashi, K. / Yoneda, S. / Yamada, M. / Kamakura, M. / Ikushiro, S. / Shiro, Y. / Sakaki, T.
CitationJournal: 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
DepositionOct 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 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)46,0253
Polymers44,9921
Non-polymers1,0332
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.152, 53.671, 138.881
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: 44991.742 Da / Num. of mol.: 1 / Mutation: 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 / Heme B


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 / Calcitriol


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


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 26% PEG MME 2000, 0.1M BIS-TRIS, 0.2M sodium chloride, pH 6.6, 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: Apr 11, 2007 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 32117 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rsym value: 0.056 / Net I/σ(I): 26.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 6.8 / Rsym value: 0.316 / % possible all: 99.9

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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 2ZBY

2zby


Resolution: 1.9→19.74 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.388 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24196 1614 5 %RANDOM
Rwork0.19802 ---
obs0.20017 30443 99.77 %-
all-30443 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.704 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20 Å2
2---0.57 Å20 Å2
3----0.63 Å2
Refine analyze
ObsFree
Luzzati coordinate error0.227 Å-
Luzzati sigma a0.085 Å0.118 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 73 319 3482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223233
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0992.0254428
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8375403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83223.566143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98215501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7851529
X-RAY DIFFRACTIONr_chiral_restr0.0710.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022479
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1840.21587
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22256
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.441.52080
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76723254
X-RAY DIFFRACTIONr_scbond_it0.97831283
X-RAY DIFFRACTIONr_scangle_it1.5754.51172
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 108 -
Rwork0.227 2185 -
obs--98.62 %

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