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- PDB-6rqb: CYP121 in complex with 3-bromo dicyclotyrosine -

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Basic information

Entry
Database: PDB / ID: 6rqb
TitleCYP121 in complex with 3-bromo dicyclotyrosine
ComponentsMycocyclosin synthase
KeywordsOXIDOREDUCTASE / CYP121 / P450 / dicyclotyrosine derivatives / heme
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 / 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
PROTOPORPHYRIN IX CONTAINING FE / 3-bromo dicyclotyrosine / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.459 Å
AuthorsPoddar, H. / Levy, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Activity Relationships of cyclo (l-Tyrosyl-l-tyrosine) Derivatives Binding to Mycobacterium tuberculosis CYP121: Iodinated Analogues Promote Shift to High-Spin Adduct.
Authors: Rajput, S. / McLean, K.J. / Poddar, H. / Selvam, I.R. / Nagalingam, G. / Triccas, J.A. / Levy, C.W. / Munro, A.W. / Hutton, C.A.
History
DepositionMay 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Mycocyclosin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7127
Polymers43,3061
Non-polymers1,4066
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-86 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.681, 77.681, 263.847
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

21A-793-

HOH

31A-822-

HOH

41A-862-

HOH

51A-907-

HOH

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Components

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


Mass: 43305.863 Da / Num. of mol.: 1 / Fragment: Mycocyclosin synthase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cyp121, MT2336 / Variant: CDC 1551 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Variant (production host): HMS174(DE3)
References: UniProt: P9WPP6, UniProt: P9WPP7*PLUS, mycocyclosin synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-Q47 / 3-bromo dicyclotyrosine


Mass: 405.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17BrN2O4 / Feature type: SUBJECT OF INVESTIGATION
#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.: 412 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 1.5 - 2.1 M Ammonium sulfate, 0.1 M MES / PH range: 5.5 - 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.459→65.96 Å / Num. obs: 82913 / % possible obs: 100 % / Redundancy: 13.8 % / Net I/σ(I): 12.6
Reflection shellResolution: 1.459→1.4764 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2432

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1N40

1n40


Resolution: 1.459→47.099 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.56
RfactorNum. reflection% reflection
Rfree0.2192 4016 4.99 %
Rwork0.189 --
obs0.1905 80495 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.26 Å2 / Biso mean: 20.0216 Å2 / Biso min: 8.31 Å2
Refinement stepCycle: final / Resolution: 1.459→47.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 113 412 3551
Biso mean--22.05 28.41 -
Num. residues----393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4592-1.47640.42761290.36972432256193
1.4764-1.49440.31781250.33532609273496
1.4944-1.51330.34421350.32082547268297
1.5133-1.53330.35511220.32472612273497
1.5333-1.55430.33261240.29442606273097
1.5543-1.57650.28261370.28422568270597
1.5765-1.60.28561150.27732587270297
1.6-1.6250.28671220.27052615273797
1.625-1.65160.28761320.26032613274597
1.6516-1.68010.29091560.2572577273397
1.6801-1.71070.28991420.23732593273597
1.7107-1.74360.22671360.23872587272397
1.7436-1.77920.25171320.2262609274197
1.7792-1.81790.26921330.22152607274097
1.8179-1.86020.2641470.20492571271897
1.8602-1.90670.21671620.19872565272796
1.9067-1.95820.22171490.19262609275897
1.9582-2.01580.22711220.18332634275697
2.0158-2.08090.2021480.18042615276397
2.0809-2.15530.22621540.17282618277297
2.1553-2.24160.21571570.16432605276297
2.2416-2.34360.19341470.16392638278597
2.3436-2.46710.17721340.16092680281498
2.4671-2.62170.22711270.16172692281997
2.6217-2.82410.19661440.16092696284098
2.8241-3.10830.22761550.17222743289899
3.1083-3.55790.18341490.16092762291198
3.5579-4.4820.15561360.14752819295599
4.482-47.12350.21281450.187730703215100

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