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- PDB-6rq6: CYP121 in complex with 3-fluoro dicyclotyrosine -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6rq6
TitleCYP121 in complex with 3-fluoro 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-fluoro dicyclotyrosine / Mycocyclosin synthase / Mycocyclosin synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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)44,9429
Polymers43,3061
Non-polymers1,6368
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-95 kcal/mol
Surface area16770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.890, 77.890, 264.020
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-555-

HOH

21A-750-

HOH

31A-804-

HOH

41A-814-

HOH

51A-818-

HOH

61A-910-

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, 421 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-R2H / 3-fluoro dicyclotyrosine


Mass: 344.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17FN2O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
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: 1.42→65.36 Å / Num. obs: 90002 / % possible obs: 99.9 % / Redundancy: 11 % / Net I/σ(I): 14.1
Reflection shellResolution: 1.42→1.436 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2765 / % possible all: 99.9

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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: 1.42→53.538 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.78
RfactorNum. reflection% reflection
Rfree0.1907 4439 4.93 %
Rwork0.1719 --
obs0.1728 90089 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.28 Å2 / Biso mean: 17.7011 Å2 / Biso min: 6.85 Å2
Refinement stepCycle: final / Resolution: 1.42→53.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 173 413 3612
Biso mean--22.83 24.85 -
Num. residues----393
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 (%)
1.42-1.43620.36631420.32827652907100
1.4362-1.45310.29171280.30828202948100
1.4531-1.47080.28231440.270728232967100
1.4708-1.48940.2711170.265928092926100
1.4894-1.5090.2981430.251528122955100
1.509-1.52970.27661570.240128232980100
1.5297-1.55150.26141550.227727962951100
1.5515-1.57470.24651520.212627952947100
1.5747-1.59930.23571580.201428012959100
1.5993-1.62550.20941460.193928442990100
1.6255-1.65350.19621470.188628032950100
1.6535-1.68360.2071510.18928142965100
1.6836-1.7160.20471510.191628032954100
1.716-1.7510.20531550.185328352990100
1.751-1.78910.19561490.175228202969100
1.7891-1.83070.18951300.169328572987100
1.8307-1.87650.19761490.173228332982100
1.8765-1.92720.18431530.169328613014100
1.9272-1.9840.18021550.169228232978100
1.984-2.0480.1891710.161328413012100
2.048-2.12120.17551290.162928622991100
2.1212-2.20610.20871600.156328583018100
2.2061-2.30650.18071540.147828613015100
2.3065-2.42810.17861480.145828943042100
2.4281-2.58030.17281280.149529063034100
2.5803-2.77950.18441490.156629173066100
2.7795-3.05920.18891370.168329213058100
3.0592-3.50180.16351630.163429323095100
3.5018-4.41150.15111670.1422935310298
4.4115-53.57560.1771510.17033186333798

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