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- PDB-5opa: The crystal structure of P450 CYP121 in complex with lead compound 7b -

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Basic information

Entry
Database: PDB / ID: 5opa
TitleThe crystal structure of P450 CYP121 in complex with lead compound 7b
ComponentsMycocyclosin synthase
KeywordsOXIDOREDUCTASE / Cytochrome P450 Inhibitor complex
Function / homology
Function and homology information


mycocyclosin synthase / 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
Chem-A2W / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.345 Å
AuthorsLevy, C.W.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Novel Aryl Substituted Pyrazoles as Small Molecule Inhibitors of Cytochrome P450 CYP121A1: Synthesis and Antimycobacterial Evaluation.
Authors: Taban, I.M. / Elshihawy, H.E.A.E. / Torun, B. / Zucchini, B. / Williamson, C.J. / Altuwairigi, D. / Ngu, A.S.T. / McLean, K.J. / Levy, C.W. / Sood, S. / Marino, L.B. / Munro, A.W. / de ...Authors: Taban, I.M. / Elshihawy, H.E.A.E. / Torun, B. / Zucchini, B. / Williamson, C.J. / Altuwairigi, D. / Ngu, A.S.T. / McLean, K.J. / Levy, C.W. / Sood, S. / Marino, L.B. / Munro, A.W. / de Carvalho, L.P.S. / Simons, C.
History
DepositionAug 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mycocyclosin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8279
Polymers43,3061
Non-polymers1,5218
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-104 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.887, 77.887, 263.547
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-875-

HOH

21A-908-

HOH

31A-920-

HOH

41A-995-

HOH

51A-1067-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mycocyclosin synthase / Cytochrome P450 121 / Cytochrome P450 MT2


Mass: 43305.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Gene: cyp121, MT2336 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPP6, EC: 1.14.21.9

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Non-polymers , 5 types, 580 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-A2W / 3-(4-fluorophenyl)-4-(imidazol-1-ylmethyl)-1-phenyl-pyrazole


Mass: 318.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15FN4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 800 nL drops with protein-to-mother liquor at a ratio of 1:1, by vapor diffusion in 1.5 to 2.1 M ammonium sulfate and 0.1 M sodium MES or Cacodylate from pH 5.5 to 6.15

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.345→53.5 Å / Num. obs: 105311 / % possible obs: 99.59 % / Redundancy: 15.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0677 / Rpim(I) all: 0.01637 / Net I/σ(I): 24.27
Reflection shellResolution: 1.345→1.393 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.5036 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 9991 / CC1/2: 0.798 / Rpim(I) all: 0.235 / % possible all: 96.27

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2807: ???)refinement
xia2data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In house model

Resolution: 1.345→53.5 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.88
RfactorNum. reflection% reflectionSelection details
Rfree0.1574 5301 5.03 %Random
Rwork0.1303 ---
obs0.1317 105317 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.345→53.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 99 572 3697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023404
X-RAY DIFFRACTIONf_angle_d1.7644674
X-RAY DIFFRACTIONf_dihedral_angle_d17.3571276
X-RAY DIFFRACTIONf_chiral_restr0.108513
X-RAY DIFFRACTIONf_plane_restr0.012609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3449-1.36020.22721730.21073084X-RAY DIFFRACTION94
1.3602-1.37620.23171560.20273180X-RAY DIFFRACTION96
1.3762-1.3930.24411480.18053263X-RAY DIFFRACTION98
1.393-1.41060.22191640.15933259X-RAY DIFFRACTION99
1.4106-1.42920.20161720.14233251X-RAY DIFFRACTION100
1.4292-1.44880.16031670.13023325X-RAY DIFFRACTION100
1.4488-1.46950.16841740.11733313X-RAY DIFFRACTION100
1.4695-1.49140.16981790.10773244X-RAY DIFFRACTION100
1.4914-1.51470.15111710.10523318X-RAY DIFFRACTION100
1.5147-1.53950.1371830.09713282X-RAY DIFFRACTION100
1.5395-1.56610.13391550.09733320X-RAY DIFFRACTION100
1.5661-1.59460.13381810.10113306X-RAY DIFFRACTION100
1.5946-1.62520.14441690.10363343X-RAY DIFFRACTION100
1.6252-1.65840.12851780.10223278X-RAY DIFFRACTION100
1.6584-1.69450.1341680.10383331X-RAY DIFFRACTION100
1.6945-1.73390.14271550.11083347X-RAY DIFFRACTION100
1.7339-1.77730.14061960.11393301X-RAY DIFFRACTION100
1.7773-1.82530.14421770.11233321X-RAY DIFFRACTION100
1.8253-1.8790.16161720.1163319X-RAY DIFFRACTION100
1.879-1.93970.13921900.1183326X-RAY DIFFRACTION100
1.9397-2.0090.16221740.12283345X-RAY DIFFRACTION100
2.009-2.08940.161780.11613344X-RAY DIFFRACTION100
2.0894-2.18450.13121880.1163363X-RAY DIFFRACTION100
2.1845-2.29970.13541860.1153358X-RAY DIFFRACTION100
2.2997-2.44380.14261820.11583400X-RAY DIFFRACTION100
2.4438-2.63250.13711850.12483371X-RAY DIFFRACTION100
2.6325-2.89740.16821900.13763422X-RAY DIFFRACTION100
2.8974-3.31660.14131840.14433449X-RAY DIFFRACTION100
3.3166-4.17850.14732010.14143498X-RAY DIFFRACTION100
4.1785-60.10290.21892050.1643755X-RAY DIFFRACTION100

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