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

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Basic information

Entry
Database: PDB / ID: 3ivy
TitleCrystal structure of Mycobacterium tuberculosis cytochrome P450 CYP125, p212121 crystal form
ComponentsCytochrome P450 CYP125
KeywordsOXIDOREDUCTASE / cholesterol / cytochrome P450 / tuberculosis / monooxygenase / 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 / Steroid C26-monooxygenase / Steroid C26-monooxygenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.352 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 23, 2015Group: Other
Revision 1.3Sep 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)49,1082
Polymers48,4911
Non-polymers6161
Water12,755708
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.030, 86.020, 89.630
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 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
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: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 1, 2007
Details: Single crystal monochromator and toroidal focusing mirror
RadiationMonochromator: Si(111) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 99798 / Num. obs: 99798 / % possible obs: 97.95 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.2
Reflection shellResolution: 1.35→1.38 Å / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2 / % possible all: 90

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CPT

1cpt


Resolution: 1.352→28.223 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 19.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2037 5013 5.02 %
Rwork0.1585 --
obs0.1608 99798 97.95 %
all-99798 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.998 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 1.352→28.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 43 708 3892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0333395
X-RAY DIFFRACTIONf_angle_d2.5284645
X-RAY DIFFRACTIONf_dihedral_angle_d17.7331229
X-RAY DIFFRACTIONf_chiral_restr0.189474
X-RAY DIFFRACTIONf_plane_restr0.017618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.352-1.36750.38921350.34562663X-RAY DIFFRACTION83
1.3675-1.38360.35551610.31953143X-RAY DIFFRACTION100
1.3836-1.40050.32481900.29083196X-RAY DIFFRACTION100
1.4005-1.41820.3251620.26723149X-RAY DIFFRACTION100
1.4182-1.43690.28711780.23963206X-RAY DIFFRACTION100
1.4369-1.45650.2691780.24663156X-RAY DIFFRACTION100
1.4565-1.47730.30451640.23423204X-RAY DIFFRACTION100
1.4773-1.49940.23441600.20773202X-RAY DIFFRACTION100
1.4994-1.52280.23281590.18793153X-RAY DIFFRACTION100
1.5228-1.54780.26651780.18573220X-RAY DIFFRACTION100
1.5478-1.57450.22831530.15993210X-RAY DIFFRACTION100
1.5745-1.60310.19821950.14363151X-RAY DIFFRACTION100
1.6031-1.63390.1811490.13753227X-RAY DIFFRACTION100
1.6339-1.66730.20351900.12483189X-RAY DIFFRACTION100
1.6673-1.70350.17491690.11493196X-RAY DIFFRACTION100
1.7035-1.74320.17041510.10813216X-RAY DIFFRACTION100
1.7432-1.78670.18351720.11473211X-RAY DIFFRACTION100
1.7867-1.8350.19791700.11413202X-RAY DIFFRACTION100
1.835-1.8890.17061790.11723213X-RAY DIFFRACTION100
1.889-1.950.21881560.15293231X-RAY DIFFRACTION100
1.95-2.01970.17291600.11873217X-RAY DIFFRACTION100
2.0197-2.10050.16331780.1033217X-RAY DIFFRACTION100
2.1005-2.19610.15661620.11323230X-RAY DIFFRACTION100
2.1961-2.31180.23271500.1513272X-RAY DIFFRACTION100
2.3118-2.45660.1651670.13673242X-RAY DIFFRACTION100
2.4566-2.64610.17791630.133247X-RAY DIFFRACTION100
2.6461-2.91210.17251930.13833236X-RAY DIFFRACTION100
2.9121-3.3330.15791760.13193247X-RAY DIFFRACTION99
3.333-4.1970.17351610.14392981X-RAY DIFFRACTION90
4.197-28.2290.21921540.19892558X-RAY DIFFRACTION74

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