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- PDB-5li6: Crystal structure of Mycobacterium tuberculosis CYP126A1 in compl... -

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Basic information

Entry
Database: PDB / ID: 5li6
TitleCrystal structure of Mycobacterium tuberculosis CYP126A1 in complex with N-isopropyl-N-((3-(4-methoxyphenyl)-1,2,4-oxadiazol-5-yl)methyl)-2-(4-nitrophenyl)acetamide
ComponentsPutative cytochrome P450 126
KeywordsOXIDOREDUCTASE / monoxygenase / cytochrome P450 / OXIDOREDUCATSE
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
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
Chem-6XF / PROTOPORPHYRIN IX CONTAINING FE / Putative cytochrome P450 126
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLevy, C. / Munro, A.W. / Leys, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I019227/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/I019669/1 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural Characterization and Ligand/Inhibitor Identification Provide Functional Insights into the Mycobacterium tuberculosis Cytochrome P450 CYP126A1.
Authors: Chenge, J.T. / Duyet, L.V. / Swami, S. / McLean, K.J. / Kavanagh, M.E. / Coyne, A.G. / Rigby, S.E. / Cheesman, M.R. / Girvan, H.M. / Levy, C.W. / Rupp, B. / von Kries, J.P. / Abell, C. / Leys, D. / Munro, A.W.
History
DepositionJul 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Jan 10, 2024Group: 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: Putative cytochrome P450 126
B: Putative cytochrome P450 126
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0766
Polymers92,0222
Non-polymers2,0544
Water15,709872
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-53 kcal/mol
Surface area29640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.620, 59.660, 118.470
Angle α, β, γ (deg.)90.00, 98.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative cytochrome P450 126


Mass: 46010.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: cyp126, MT0802 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WPN8, 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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-6XF / ~{N}-[[3-(4-methoxyphenyl)-1,2,4-oxadiazol-5-yl]methyl]-2-(4-nitrophenyl)-~{N}-propan-2-yl-ethanamide


Mass: 410.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H22N4O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 872 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M carboxylic acids, 0.1M imidazole-MES pH 6.5, 30% PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→32.14 Å / Num. obs: 66993 / % possible obs: 99.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 11.9
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.842 / Mean I/σ(I) obs: 1.8 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXA

1oxa


Resolution: 1.95→32.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.655 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.154 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24174 3560 5 %RANDOM
Rwork0.18568 ---
obs0.18851 66993 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 16.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20.19 Å2
2---0.5 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.95→32.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5930 0 146 872 6948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226262
X-RAY DIFFRACTIONr_bond_other_d0.0010.024294
X-RAY DIFFRACTIONr_angle_refined_deg1.7752.0138540
X-RAY DIFFRACTIONr_angle_other_deg1.0343.00110272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8425755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.8322.133300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89215981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7441576
X-RAY DIFFRACTIONr_chiral_restr0.1140.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021346
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_it1.0371.53760
X-RAY DIFFRACTIONr_mcbond_other0.3051.51523
X-RAY DIFFRACTIONr_mcangle_it1.8126054
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.03532502
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7034.52483
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.946→1.996 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 255 -
Rwork0.316 4759 -
obs--100 %

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