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- PDB-3a4g: Structure of cytochrome P450 vdh from Pseudonocardia autotrophica... -

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Basic information

Entry
Database: PDB / ID: 3a4g
TitleStructure of cytochrome P450 vdh from Pseudonocardia autotrophica (trigonal crystal form)
ComponentsVitamin D hydroxylase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / vitamin D3 hydroxylase / hemoprotein / Monooxygenase
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: 1.75 Å
AuthorsYasutake, Y. / Fujii, Y. / Cheon, W.K. / Arisawa, A. / Tamura, T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural evidence for enhancement of sequential vitamin D3 hydroxylation activities by directed evolution of cytochrome P450 vitamin D3 hydroxylase
Authors: Yasutake, Y. / Fujii, Y. / Nishioka, T. / Cheon, W.K. / Arisawa, A. / Tamura, T.
History
DepositionJul 7, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitamin D hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2243
Polymers45,4881
Non-polymers7372
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.675, 61.675, 98.799
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 hydroxylase


Mass: 45487.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonocardia autotrophica (bacteria) / Strain: NBRC 12743 / Gene: vdh / Plasmid: pTip-QC2 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): L88 / References: UniProt: C4B644
#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.: 338 / 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: 2.38 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 38% PEG400, 0.1M Bis-tris, pH7.5, 50mM CaCl2, 60mM NaCl, 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 315r / Detector: CCD / Date: May 19, 2006
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: 1.75→50 Å / Num. all: 42012 / Num. obs: 42012 / % possible obs: 99.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.9
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3957 / % possible all: 93.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JIN

1jin


Resolution: 1.75→29.44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.325 / SU ML: 0.077 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23624 2072 4.9 %RANDOM
Rwork0.18501 ---
obs0.18748 39901 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.704 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.3 Å20 Å2
2--0.61 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 51 338 3451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223185
X-RAY DIFFRACTIONr_angle_refined_deg1.5312.034345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0175394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43223.217143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9115514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1941532
X-RAY DIFFRACTIONr_chiral_restr0.0990.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022451
X-RAY DIFFRACTIONr_nbd_refined0.2130.21637
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22191
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.231
X-RAY DIFFRACTIONr_mcbond_it1.0881.52017
X-RAY DIFFRACTIONr_mcangle_it1.78323185
X-RAY DIFFRACTIONr_scbond_it2.48731293
X-RAY DIFFRACTIONr_scangle_it3.8824.51158
LS refinement shellResolution: 1.751→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 127 -
Rwork0.237 2688 -
obs--100 %

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