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- PDB-3vrm: Structure of cytochrome P450 Vdh mutant T107A with bound vitamin D3 -

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Basic information

Entry
Database: PDB / ID: 3vrm
TitleStructure of cytochrome P450 Vdh mutant T107A with bound vitamin D3
ComponentsVitamin D(3) 25-hydroxylase
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 / VITAMIN D3 / MONOOXYGENASE / P450 fold / Hemoprotein
Function / homology
Function and homology information


cholestanetriol 26-monooxygenase / cholestanetetraol 26-dehydrogenase activity / 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-VD3 / Vitamin D(3) 25-hydroxylase
Similarity search - Component
Biological speciesPseudonocardia autotrophica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsNishioka, T. / Yasutake, Y. / Tamura, T.
CitationJournal: Chembiochem / Year: 2013
Title: A single mutation at the ferredoxin binding site of p450 vdh enables efficient biocatalytic production of 25-hydroxyvitamin d3.
Authors: Yasutake, Y. / Nishioka, T. / Imoto, N. / Tamura, T.
History
DepositionApr 12, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin D(3) 25-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4593
Polymers45,4581
Non-polymers1,0012
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.421, 105.521, 141.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Vitamin D(3) 25-hydroxylase / Cytochrome P450


Mass: 45457.578 Da / Num. of mol.: 1 / Mutation: T107A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia autotrophica (bacteria) / Strain: NBRC 12743 / Gene: vdh / Plasmid: PET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4B644, EC: 1.14.13.15
#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-VD3 / (1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6-METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLI DENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL / VITAMIN D3


Mass: 384.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Description: The entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 21% PEG 3350, 0.2M NaCl, 0.1M bis-tris, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 29, 2011
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 14156 / % possible obs: 98.6 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.2
Reflection shellResolution: 2.57→2.72 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.05 / Num. unique all: 4213 / % possible all: 92.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A50

3a50


Resolution: 2.57→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 23.368 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 0.807 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: the entry contains Friedel pairs in F_Plus/Minus columns. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 741 5 %RANDOM
Rwork0.18681 ---
obs0.18906 14156 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.693 Å2
Baniso -1Baniso -2Baniso -3
1--3.43 Å2-0 Å20 Å2
2--6.74 Å2-0 Å2
3----3.31 Å2
Refinement stepCycle: LAST / Resolution: 2.57→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 71 36 3212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9342.0254485
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6445401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.6523.217143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.22615519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4731532
X-RAY DIFFRACTIONr_chiral_restr0.0840.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212509
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.569→2.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 33 -
Rwork0.305 805 -
obs--83.3 %
Refinement TLS params.Method: refined / Origin x: 11.2528 Å / Origin y: 24.5383 Å / Origin z: 17.9473 Å
111213212223313233
T0.0779 Å2-0.0087 Å2-0.0003 Å2-0.1908 Å20.0163 Å2--0.0462 Å2
L4.7688 °20.3654 °22.6227 °2-1.4214 °20.5316 °2--4.1456 °2
S0.0198 Å °-0.5803 Å °-0.0278 Å °0.2973 Å °0.021 Å °0.0805 Å °-0.0239 Å °-0.2321 Å °-0.0408 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 100
2X-RAY DIFFRACTION1A101 - 239
3X-RAY DIFFRACTION1A240 - 403

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