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

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Basic information

Entry
Database: PDB / ID: 5ibi
TitleCrystal structure Mycobacterium tuberculosis CYP121 in complex with inhibitor fragment 26a
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 / cholest-4-en-3-one 26-monooxygenase activity / carbon monoxide binding / steroid hydroxylase activity / cholesterol catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity ...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 / cholest-4-en-3-one 26-monooxygenase activity / carbon monoxide binding / steroid hydroxylase activity / cholesterol catabolic process / 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-69U / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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Assembly

Deposited unit
A: Cytochrome P450 121 CYP121
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5846
Polymers43,3061
Non-polymers1,2785
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-67 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.822, 77.822, 265.088
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-597-

HOH

21A-826-

HOH

31A-892-

HOH

41A-930-

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-69U / 4,4'-(5-{[(4-hydroxyphenyl)methyl]amino}-1H-pyrazole-3,4-diyl)diphenol


Mass: 373.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19N3O3
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
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 5.5-6.1
PH range: 5.5 - 6.15

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→47.254 Å / Num. obs: 45602 / % possible obs: 99.93 % / Redundancy: 12.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.1615 / Net I/σ(I): 11.49
Reflection shellResolution: 2.2→2.278 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.2824 / Mean I/σ(I) obs: 7.3 / % possible all: 99.35

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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: 2.2→47.254 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 20.06
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 3641 7.98 %Random
Rwork0.194 ---
obs0.1971 45602 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→47.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 86 436 3535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043217
X-RAY DIFFRACTIONf_angle_d1.0374399
X-RAY DIFFRACTIONf_dihedral_angle_d13.0081198
X-RAY DIFFRACTIONf_chiral_restr0.035499
X-RAY DIFFRACTIONf_plane_restr0.007567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1996-2.22850.291380.22251619X-RAY DIFFRACTION98
2.2285-2.25910.29651370.23181586X-RAY DIFFRACTION100
2.2591-2.29130.27021480.21721646X-RAY DIFFRACTION100
2.2913-2.32550.26051390.22641577X-RAY DIFFRACTION100
2.3255-2.36190.23911420.2191653X-RAY DIFFRACTION100
2.3619-2.40060.29891340.22441584X-RAY DIFFRACTION100
2.4006-2.4420.27441370.22871647X-RAY DIFFRACTION100
2.442-2.48640.30811380.22741589X-RAY DIFFRACTION100
2.4864-2.53420.28661420.21821614X-RAY DIFFRACTION100
2.5342-2.58590.28381420.22161634X-RAY DIFFRACTION100
2.5859-2.64220.2591400.22261607X-RAY DIFFRACTION100
2.6422-2.70360.29691420.22761603X-RAY DIFFRACTION100
2.7036-2.77120.23061300.21121620X-RAY DIFFRACTION100
2.7712-2.84610.24761370.2161600X-RAY DIFFRACTION100
2.8461-2.92990.23721430.21691624X-RAY DIFFRACTION100
2.9299-3.02440.22611400.21171622X-RAY DIFFRACTION100
3.0244-3.13250.24691430.21281611X-RAY DIFFRACTION100
3.1325-3.25790.26761450.19971614X-RAY DIFFRACTION100
3.2579-3.40610.2011390.18771614X-RAY DIFFRACTION100
3.4061-3.58560.20361420.17021602X-RAY DIFFRACTION100
3.5856-3.81020.1831450.15851610X-RAY DIFFRACTION100
3.8102-4.10420.19051400.1541633X-RAY DIFFRACTION100
4.1042-4.5170.14341430.13971592X-RAY DIFFRACTION100
4.517-5.16990.18871460.14621625X-RAY DIFFRACTION100
5.1699-6.51080.231370.17851621X-RAY DIFFRACTION100
6.5108-47.26460.17011320.16171614X-RAY DIFFRACTION100

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