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- PDB-3a4h: Structure of cytochrome P450 vdh from Pseudonocardia autotrophica... -

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Basic information

Entry
Database: PDB / ID: 3a4h
TitleStructure of cytochrome P450 vdh from Pseudonocardia autotrophica (orthorhombic 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: 3.06 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_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)46,1443
Polymers45,4881
Non-polymers6572
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.595, 65.793, 102.264
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 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% PEG1000, 0.1M Bis-tris, pH7.5, 50mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 22, 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: 3.05→50 Å / Num. all: 8366 / Num. obs: 8366 / % possible obs: 97.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.9
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 6 / Num. unique all: 822 / % possible all: 97.9

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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 3A4G

3a4g


Resolution: 3.06→45.74 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.868 / SU B: 23.252 / SU ML: 0.421 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26978 430 5.2 %RANDOM
Rwork0.21672 ---
obs0.21952 7852 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.138 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å20 Å20 Å2
2--7.4 Å20 Å2
3----3.58 Å2
Refinement stepCycle: LAST / Resolution: 3.06→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 44 0 3138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223210
X-RAY DIFFRACTIONr_angle_refined_deg0.962.0274384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3435399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86923.217143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49415518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3751532
X-RAY DIFFRACTIONr_chiral_restr0.0620.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022471
X-RAY DIFFRACTIONr_nbd_refined0.180.21481
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22170
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.22
X-RAY DIFFRACTIONr_mcbond_it0.3231.52043
X-RAY DIFFRACTIONr_mcangle_it0.58523226
X-RAY DIFFRACTIONr_scbond_it0.4631295
X-RAY DIFFRACTIONr_scangle_it0.8134.51156
LS refinement shellResolution: 3.058→3.138 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 45 -
Rwork0.308 546 -
obs--96.73 %

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