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- PDB-3iw0: Crystal structure of Mycobacterium tuberculosis cytochrome P450 C... -

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Basic information

Entry
Database: PDB / ID: 3iw0
TitleCrystal structure of Mycobacterium tuberculosis cytochrome P450 CYP125, C2221 crystal form
ComponentsCytochrome P450 CYP125
KeywordsOXIDOREDUCTASE / cholesterol / cytochrome P450 / monooxygenase / tuberculosis / Heme / Iron / Metal-binding
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming] / cholest-4-en-3-one 26-monooxygenase activity / biological process involved in interaction with host / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / Steroid C26-monooxygenase / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMcLean, K.J. / Levy, C. / Munro, A.W. / Leys, D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The Structure of Mycobacterium tuberculosis CYP125: molecular basis for cholesterol binding in a P450 needed for host infection.
Authors: McLean, K.J. / Lafite, P. / Levy, C. / Cheesman, M.R. / Mast, N. / Pikuleva, I.A. / Leys, D. / Munro, A.W.
History
DepositionSep 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cytochrome P450 CYP125
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2033
Polymers48,4911
Non-polymers7112
Water12,574698
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.500, 118.900, 145.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-457-

HOH

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Components

#1: Protein Cytochrome P450 CYP125


Mass: 48491.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Protein was produced in E.coli HMS174(DE3) (typically 15-20 L, grown in 2YT media) by IPTG (0.15 mM) induction in presence of the heme precursor delta aminolevulinic acid (delALA, 0.1 mM) at ...Details: Protein was produced in E.coli HMS174(DE3) (typically 15-20 L, grown in 2YT media) by IPTG (0.15 mM) induction in presence of the heme precursor delta aminolevulinic acid (delALA, 0.1 mM) at OD600 = 0.6, with temperature then reduced from 37 deg C to 23 deg C and culture continued for 24 hrs.
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: cyp125, MT3649, MTCY03C7.11, Rv3545c / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: P63709, UniProt: P9WPP1*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystallization was refined to two different conditions, both consisting of MgCl2 with 0.1 M HEPES (either pH 7.0 or 7.5) and 20% PEG 6000 or 25% PEG 3350, respectively., VAPOR DIFFUSION, ...Details: Crystallization was refined to two different conditions, both consisting of MgCl2 with 0.1 M HEPES (either pH 7.0 or 7.5) and 20% PEG 6000 or 25% PEG 3350, respectively., VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2008
Details: Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focusing
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 49511 / Num. obs: 49511 / % possible obs: 99.38 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.4
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IVY

3ivy


Resolution: 1.7→29.37 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.853 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18885 2689 5.2 %RANDOM
Rwork0.15413 ---
all0.15595 49511 --
obs0.15595 49511 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.769 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.89 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 48 698 3929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223393
X-RAY DIFFRACTIONr_bond_other_d0.0010.022271
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9794642
X-RAY DIFFRACTIONr_angle_other_deg0.95135514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81624.061165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35415527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6731523
X-RAY DIFFRACTIONr_chiral_restr0.0760.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
X-RAY DIFFRACTIONr_nbd_refined0.2330.2819
X-RAY DIFFRACTIONr_nbd_other0.1990.22502
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21677
X-RAY DIFFRACTIONr_nbtor_other0.0830.21622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2485
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9321.52244
X-RAY DIFFRACTIONr_mcbond_other0.2081.5840
X-RAY DIFFRACTIONr_mcangle_it1.25823343
X-RAY DIFFRACTIONr_scbond_it2.10931460
X-RAY DIFFRACTIONr_scangle_it2.9614.51288
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 208 -
Rwork0.218 3601 -
obs--99.76 %

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