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- PDB-4g48: Structure of CYP121 in complex with 4-(4-phenoxy-1H-pyrazol-3-yl)... -

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Basic information

Entry
Database: PDB / ID: 4g48
TitleStructure of CYP121 in complex with 4-(4-phenoxy-1H-pyrazol-3-yl)benzene-1,3-diol
ComponentsCytochrome P450 121
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / P450 / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


mycocyclosin synthase / cyclase activity / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / carbon monoxide binding / monooxygenase activity / oxidoreductase 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
PROTOPORPHYRIN IX CONTAINING FE / 4-(4-phenoxy-1H-pyrazol-3-yl)benzene-1,3-diol / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsHudson, S.A. / McLean, K.J. / Surade, S. / Yang, Y.-Q. / Leys, D. / Ciulli, A. / Munro, A.W. / Abell, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Application of Fragment Screening and Merging to the Discovery of Inhibitors of the Mycobacterium tuberculosis Cytochrome P450 CYP121
Authors: Hudson, S.A. / McLean, K.J. / Surade, S. / Yang, Y.-Q. / Leys, D. / Ciulli, A. / Munro, A.W. / Abell, C.
History
DepositionJul 16, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4796
Polymers43,3061
Non-polymers1,1735
Water10,827601
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cytochrome P450 121
hetero molecules

A: Cytochrome P450 121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,95812
Polymers86,6122
Non-polymers2,34610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area2170 Å2
ΔGint-12 kcal/mol
Surface area31560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.730, 77.730, 263.380
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-666-

HOH

21A-709-

HOH

31A-904-

HOH

41A-922-

HOH

51A-925-

HOH

61A-993-

HOH

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Components

#1: Protein 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 (bacteria) / Strain: H37Rv / Gene: Rv2276 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A514, UniProt: P9WPP7*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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PZB / 4-(4-phenoxy-1H-pyrazol-3-yl)benzene-1,3-diol


Mass: 268.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 53.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2M ammonium sulphate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→47.071 Å / Num. all: 76377 / Num. obs: 76377 / % possible obs: 99.99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.23 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→47.071 Å / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.904 / SU ML: 0.19 / σ(F): 0 / Phase error: 16.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 1990 2.61 %
Rwork0.1708 --
all0.1713 76377 -
obs0.1713 76377 99.99 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.51 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 66.46 Å2 / Biso mean: 18.943 Å2 / Biso min: 7.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.0096 Å20 Å20 Å2
2--0.0096 Å2-0 Å2
3----0.0193 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 78 601 3664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063241
X-RAY DIFFRACTIONf_angle_d1.0494437
X-RAY DIFFRACTIONf_chiral_restr0.069514
X-RAY DIFFRACTIONf_plane_restr0.005568
X-RAY DIFFRACTIONf_dihedral_angle_d11.691206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.53750.28261380.271651835321
1.5375-1.57910.27111390.256452015340
1.5791-1.62560.25111410.234852315372
1.6256-1.6780.23721390.221952055344
1.678-1.7380.20471400.198252415381
1.738-1.80760.23111400.17352515391
1.8076-1.88990.1961400.167652365376
1.8899-1.98950.2191420.166452775419
1.9895-2.11420.21111410.16452825423
2.1142-2.27740.18331420.15552925434
2.2774-2.50660.1771430.158253605503
2.5066-2.86920.18191430.161253755518
2.8692-3.61470.16271470.156654485595
3.6147-47.09410.1661550.163458055960

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