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- PDB-5gnl: Cytochrome P450 Vdh (CYP107BR1) F106V mutant -

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Basic information

Entry
Database: PDB / ID: 5gnl
TitleCytochrome P450 Vdh (CYP107BR1) F106V mutant
ComponentsVitamin D(3) 25-hydroxylase
KeywordsOXIDOREDUCTASE / cytochrome P450
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 / Vitamin D(3) 25-hydroxylase
Similarity search - Component
Biological speciesPseudonocardia autotrophica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYasutake, Y. / Tamura, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
NEDO Japan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structural insights into the mechanism of the drastic changes in enzymatic activity of the cytochrome P450 vitamin D3 hydroxylase (CYP107BR1) caused by a mutation distant from the active site
Authors: Yasutake, Y. / Kameda, T. / Tamura, T.
History
DepositionJul 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,1763
Polymers45,4401
Non-polymers7372
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-26 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.670, 61.670, 98.166
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Vitamin D(3) 25-hydroxylase / Cytochrome P450 / CYP107BR1


Mass: 45439.562 Da / Num. of mol.: 1 / Mutation: F106V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia autotrophica (bacteria) / Gene: vdh / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3)-RIL
References: UniProt: C4B644, cholestanetriol 26-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-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Bis-tris, 25-75 mM NaCl, 50 mM CaCl2, 38-42% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 30377 / % possible obs: 99.6 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 46
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 3.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A4G

3a4g


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.122 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.156 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23416 1522 5 %RANDOM
Rwork0.19957 ---
obs0.20129 28831 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.501 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.44 Å20 Å2
2--0.89 Å20 Å2
3----2.88 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3058 0 51 117 3226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193180
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5362.0064337
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70923.239142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34415514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8791532
X-RAY DIFFRACTIONr_chiral_restr0.1010.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212438
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_it0.8512.2251579
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4633.3331972
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9852.3351601
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.2719.2454944
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 125 -
Rwork0.304 2133 -
obs--99.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9173-2.2421.63663.5589-0.95244.96060.16830.36990.1111-0.6756-0.1432-0.35990.1550.5554-0.02520.2716-0.00140.10640.0759-0.01580.1462.4203-4.72-7.7898
25.1165-2.98092.61123.3802-1.79192.120.12270.5160.3849-0.3392-0.402-0.3219-0.58070.50030.27930.678-0.1658-0.04610.1457-0.01220.2932.653320.49441.6397
31.3967-0.71980.49942.7876-0.37162.0656-0.0615-0.1340.106-0.145-0.01540.0587-0.3559-0.04140.07690.1683-0.00180.01730.0187-0.02780.1041-3.890111.06061.7231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 83
2X-RAY DIFFRACTION2A84 - 184
3X-RAY DIFFRACTION3A185 - 403

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