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- PDB-6rq3: CYP121 in complex with 2,6-dimethyl dicyclotyrosine -

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Basic information

Entry
Database: PDB / ID: 6rq3
TitleCYP121 in complex with 2,6-dimethyl 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 / Chem-OUC / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

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Assembly

Deposited unit
A: Mycocyclosin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9529
Polymers43,3061
Non-polymers1,6468
Water7,710428
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-91 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.380, 77.380, 263.731
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-590-

HOH

21A-818-

HOH

31A-833-

HOH

41A-927-

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 / 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

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Non-polymers , 5 types, 436 molecules

#2: Chemical ChemComp-OUC / (3~{S},6~{S})-3-[(2,6-dimethyl-4-oxidanyl-phenyl)methyl]-6-[(4-hydroxyphenyl)methyl]piperazine-2,5-dione


Mass: 354.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N2O4 / Feature type: SUBJECT OF INVESTIGATION
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / 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: Mar 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→67.01 Å / Num. obs: 74788 / % possible obs: 99.1 % / Redundancy: 4.6 % / Net I/σ(I): 5.3
Reflection shellResolution: 1.5→1.5375 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5089 / % possible all: 98.4

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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: 1.5→64.949 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.76
RfactorNum. reflection% reflection
Rfree0.1962 2000 2.67 %
Rwork0.1845 --
obs0.1848 74779 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.87 Å2 / Biso mean: 18.1853 Å2 / Biso min: 6.92 Å2
Refinement stepCycle: final / Resolution: 1.5→64.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 149 428 3608
Biso mean--23.1 25.14 -
Num. residues----394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53750.24221390.22015089522898
1.5375-1.57910.24851420.225100524298
1.5791-1.62560.25631390.21535097523699
1.6256-1.6780.25261420.21315132527499
1.678-1.7380.25921380.20355036517498
1.738-1.80760.24771400.19065100524098
1.8076-1.88990.21651390.18755068520797
1.8899-1.98950.1741430.17775164530799
1.9895-2.11420.19491410.17945181532299
2.1142-2.27740.19181450.17015261540699
2.2774-2.50660.18741450.168252505395100
2.5066-2.86930.18361450.18185303544899
2.8693-3.6150.1881480.1815375552399
3.615-65.01010.17071540.18375623577798

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