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- PDB-5ibh: Crystal structure Mycobacterium tuberculosis CYP121 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5ibh
TitleCrystal structure Mycobacterium tuberculosis CYP121 in complex with inhibitor fragment 26h
ComponentsCytochrome P450 121 CYP121
KeywordsOXIDOREDUCTASE / Mycobacterium tuberculosis CYP121 Fragment based inhibitor screening
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 / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / carbon monoxide binding / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / 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
Chem-69R / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0201 Å
AuthorsLevy, C.
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
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 2.0May 1, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 121 CYP121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9057
Polymers43,3061
Non-polymers1,5996
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-69 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.140, 77.140, 267.270
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-754-

HOH

21A-816-

HOH

31A-824-

HOH

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Components

#1: Protein Cytochrome P450 121 CYP121 / P450 heme-thiolate protein Cyp121


Mass: 43305.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: cyp121, cyp121_1, EI32_2700, ERS007657_00455, ERS007661_00083, ERS007663_02869, ERS007665_01035, ERS007670_00377, ERS007672_00334, ERS007679_00173, ERS007681_01277, ERS007703_02339, ERS007720_ ...Gene: cyp121, cyp121_1, EI32_2700, ERS007657_00455, ERS007661_00083, ERS007663_02869, ERS007665_01035, ERS007670_00377, ERS007672_00334, ERS007679_00173, ERS007681_01277, ERS007703_02339, ERS007720_01219, ERS007722_01069, ERS013447_00077, ERS013471_02812, ERS023446_00317, ERS024276_01833, ERS027644_00398, ERS027652_00994, ERS027654_01464, ERS027656_01022, ERS027659_00311, ERS027666_00100, ERS031537_01827, ERS075357_02976, ERS075361_02508, ERS075387_01689, ERS124361_02646, HX90_2763
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0T9WNE5, UniProt: P9WPP7*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / 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-69R / 4,4'-(5-{[(1H-imidazol-4-yl)methyl]amino}-1H-pyrazole-3,4-diyl)diphenol


Mass: 347.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H17N5O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 53.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.5-2.1 M ammonium sulfate and 0.1 M sodium MES or Cacodylate from pH 5.5-6.15
PH range: 5.5 - 6.15

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.02→35.395 Å / Num. obs: 32000 / % possible obs: 99.99 % / Redundancy: 19.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Net I/σ(I): 20.61
Reflection shellResolution: 2.02→2.092 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.7698 / Mean I/σ(I) obs: 5.36 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INHOUSE

Resolution: 2.0201→35.395 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.87
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 1581 4.94 %Random
Rwork0.1767 ---
obs0.1781 32000 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.0201→35.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 110 333 3449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073189
X-RAY DIFFRACTIONf_angle_d1.2074361
X-RAY DIFFRACTIONf_dihedral_angle_d14.0991164
X-RAY DIFFRACTIONf_chiral_restr0.042486
X-RAY DIFFRACTIONf_plane_restr0.006566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0201-2.08530.25591440.19052727X-RAY DIFFRACTION100
2.0853-2.15980.21951130.18212706X-RAY DIFFRACTION100
2.1598-2.24630.21331380.17352680X-RAY DIFFRACTION100
2.2463-2.34850.2461220.17322728X-RAY DIFFRACTION100
2.3485-2.47230.19951720.17442689X-RAY DIFFRACTION100
2.4723-2.62710.20251390.1792722X-RAY DIFFRACTION100
2.6271-2.82990.20051600.17862722X-RAY DIFFRACTION100
2.8299-3.11450.1991450.19492759X-RAY DIFFRACTION100
3.1145-3.56480.24781390.17842800X-RAY DIFFRACTION100
3.5648-4.48990.1741500.1562839X-RAY DIFFRACTION100
4.4899-35.40070.18941590.18383047X-RAY DIFFRACTION100

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