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- PDB-5edt: Crystal structure of Mycobacterium tuberculosis CYP121 in complex... -

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Basic information

Entry
Database: PDB / ID: 5edt
TitleCrystal structure of Mycobacterium tuberculosis CYP121 in complex with LIG9
ComponentsCytochrome P450 121
KeywordsOXIDOREDUCTASE / cytochrome P450 / CYP121 / Mycobacterium tuberculosis / fragment-based drug discovery
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase 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
2-azanyl-5-chloranyl-benzamide / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 121
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKavanagh, M.E. / Coyne, A.G. / McLean, K.J. / James, G.G. / Levy, C. / Marino, L.B. / Carvalho, L.P.D. / Chan, D.S.H. / Hudson, S.A. / Surade, S. ...Kavanagh, M.E. / Coyne, A.G. / McLean, K.J. / James, G.G. / Levy, C. / Marino, L.B. / Carvalho, L.P.D. / Chan, D.S.H. / Hudson, S.A. / Surade, S. / Munro, A.W. / Abell, C.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I019669/1 United Kingdom
University of CambridgeCambridge Commonwealth Trust and Cambridge Overseas Trust United Kingdom
CitationJournal: J.Med.Chem. / Year: 2016
Title: Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors.
Authors: Kavanagh, M.E. / Coyne, A.G. / McLean, K.J. / James, G.G. / Levy, C.W. / Marino, L.B. / de Carvalho, L.P. / Chan, D.S. / Hudson, S.A. / Surade, S. / Leys, D. / Munro, A.W. / Abell, C.
History
DepositionOct 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Nov 21, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 2.2Jan 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: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,92213
Polymers43,1751
Non-polymers1,74812
Water3,927218
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-162 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.000, 77.000, 263.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

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Components

#1: Protein Cytochrome P450 121 / Cytochrome P450 MT2


Mass: 43174.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: cyp121, Mb2299 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P0A515, 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-5MK / 2-azanyl-5-chloranyl-benzamide


Mass: 170.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7ClN2O
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2M AMMONIUM SULFATE, 0.1M SODIUM CACODYLATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Sep 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→7.1 Å / Num. all: 591452 / Num. obs: 18202 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 32 % / Rsym value: 0.08 / Net I/σ(I): 16
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 9.77 % / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XPREPdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KTF

4ktf


Resolution: 2.45→7.1 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.836 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24349 895 4.9 %RANDOM
Rwork0.18743 ---
obs0.19029 17218 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.952 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.45→7.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 104 218 3323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193185
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2582.0224359
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9265393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.49223.016126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58315509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7841529
X-RAY DIFFRACTIONr_chiral_restr0.110.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0222386
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.437→2.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 45 -
Rwork0.246 1010 -
obs--93.69 %

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