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- PDB-6rq8: CYP121 in complex with 3-iodo dicyclotyrosine -

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Basic information

Entry
Database: PDB / ID: 6rq8
TitleCYP121 in complex with 3-iodo 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 / 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 ...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 / 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
PROTOPORPHYRIN IX CONTAINING FE / Chem-KEH / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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)45,0509
Polymers43,3061
Non-polymers1,7448
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-75 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.770, 77.770, 263.870
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-589-

HOH

21A-816-

HOH

31A-835-

HOH

41A-838-

HOH

51A-929-

HOH

61A-951-

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, 462 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-KEH / (3~{S},6~{S})-3-[(4-hydroxyphenyl)methyl]-6-[(3-iodanyl-4-oxidanyl-phenyl)methyl]piperazine-2,5-dione


Mass: 452.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17IN2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
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: 1.41→65.97 Å / Num. obs: 91685 / % possible obs: 99.8 % / Redundancy: 11.2 % / Net I/σ(I): 13.7
Reflection shellResolution: 1.41→1.426 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2727

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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: 1.41→53.474 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.1
RfactorNum. reflection% reflection
Rfree0.1798 4524 4.93 %
Rwork0.1611 --
obs0.162 91684 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.35 Å2 / Biso mean: 16.4631 Å2 / Biso min: 6.36 Å2
Refinement stepCycle: final / Resolution: 1.41→53.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 148 454 3633
Biso mean--23.18 24.53 -
Num. residues----394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.41-1.4260.2441350.27212727286296
1.426-1.44280.30211380.27032841297999
1.4428-1.46040.27341450.248728492994100
1.4604-1.47890.22331280.232328632991100
1.4789-1.49830.24981350.219929003035100
1.4983-1.51890.22231600.208828172977100
1.5189-1.54060.21871490.201928543003100
1.5406-1.56360.22751770.187428503027100
1.5636-1.5880.22611400.17928833023100
1.588-1.6140.20551520.175828432995100
1.614-1.64190.18681630.166428543017100
1.6419-1.67170.18031350.167228793014100
1.6717-1.70390.18121660.164928783044100
1.7039-1.73870.18231490.159428693018100
1.7387-1.77650.16551610.156228743035100
1.7765-1.81780.18661320.149929033035100
1.8178-1.86330.17791520.155728793031100
1.8633-1.91360.17651540.15428823036100
1.9136-1.970.1611570.154728813038100
1.97-2.03350.18181670.149728953062100
2.0335-2.10620.16411430.148629383081100
2.1062-2.19060.16471570.142428873044100
2.1906-2.29030.1791580.140429443102100
2.2903-2.4110.16321500.136829133063100
2.411-2.56210.16361340.139929503084100
2.5621-2.75990.18171470.149529753122100
2.7599-3.03760.18181460.16529873133100
3.0376-3.47710.15781630.159929943157100
3.4771-4.38040.15281760.143330593235100
4.3804-53.51270.19311550.169532923447100

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