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- PDB-6rq5: CYP121 in complex with 3,5-dimethyl dicyclotyrosine -

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Basic information

Entry
Database: PDB / ID: 6rq5
TitleCYP121 in complex with 3,5-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-KEB / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)44,8568
Polymers43,3061
Non-polymers1,5507
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-75 kcal/mol
Surface area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.710, 76.710, 262.300
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-805-

HOH

21A-813-

HOH

31A-894-

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, 403 molecules

#2: 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
#3: Chemical ChemComp-KEB / (3~{S},6~{S})-3-[(3,5-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
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
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: 1.55→66.43 Å / Num. obs: 65489 / % possible obs: 98 % / Redundancy: 4.8 % / Net I/σ(I): 7.7
Reflection shellResolution: 1.55→1.588 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4368

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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: 1.55→66.43 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.17
RfactorNum. reflection% reflection
Rfree0.2034 1998 3.05 %
Rwork0.1761 --
obs0.177 65489 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.37 Å2 / Biso mean: 15.3387 Å2 / Biso min: 4.34 Å2
Refinement stepCycle: final / Resolution: 1.55→66.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 170 396 3597
Biso mean--23.17 21.1 -
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 (%)
1.55-1.58880.30331380.28484368450696
1.5888-1.63170.29931380.2374401453996
1.6317-1.67970.24381400.21044443458397
1.6797-1.7340.23421390.19464400453996
1.734-1.79590.25451400.18074442458296
1.7959-1.86790.22831390.18194433457297
1.8679-1.95290.22551390.17754401454096
1.9529-2.05580.22461390.17764403454296
2.0558-2.18470.17561410.16834538467998
2.1847-2.35330.18131440.15644551469598
2.3533-2.59020.17521440.16154612475699
2.5902-2.9650.20651480.17544689483799
2.965-3.73550.18751500.17474754490499
3.7355-66.49390.18371590.16395056521599

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