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- PDB-7noy: Crystal structure of the heterocyclic toxin methyltransferase fro... -

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Basic information

Entry
Database: PDB / ID: 7noy
TitleCrystal structure of the heterocyclic toxin methyltransferase from Mycobacterium tuberculosis in complex with substrate 1-hydroxyquinolin-4(1H)-one
ComponentsUncharacterized protein Rv0560c
KeywordsTRANSFERASE / Methyltransferase / HQNO-detoxification / SAM-dependent
Function / homology
Function and homology information


2-heptyl-1-hydroxyquinolin-4(1H)-one methyltransferase / response to salicylic acid / cellular response to iron ion starvation / methyltransferase activity / methylation / response to hypoxia / cytosol
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / 1-oxidanylquinolin-4-one / 2-heptyl-1-hydroxyquinolin-4(1H)-one methyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDenkhaus, L. / Sartor, P. / Einsle, O. / Gerhardt, S. / Fetzner, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FE 383/25-1 Germany
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Structural basis of O-methylation of (2-heptyl-)1-hydroxyquinolin-4(1H)-one and related compounds by the heterocyclic toxin methyltransferase Rv0560c of Mycobacterium tuberculosis.
Authors: Sartor, P. / Denkhaus, L. / Gerhardt, S. / Einsle, O. / Fetzner, S.
History
DepositionFeb 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 6, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Rv0560c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0356
Polymers26,4201
Non-polymers6155
Water5,080282
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-25 kcal/mol
Surface area9930 Å2
Unit cell
Length a, b, c (Å)70.086, 70.086, 95.048
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Uncharacterized protein Rv0560c


Mass: 26420.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv0560c / Plasmid: pET28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta pLysSRARE / References: UniProt: P9WKL5
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-UK5 / 1-oxidanylquinolin-4-one


Mass: 161.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tacsimate pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000043 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000043 Å / Relative weight: 1
ReflectionResolution: 1.508→60.696 Å / Num. obs: 42031 / % possible obs: 98.1 % / Redundancy: 10.6 % / Biso Wilson estimate: 20.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.8
Reflection shellResolution: 1.508→1.541 Å / Num. unique obs: 2104 / CC1/2: 0.742

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BGG

7bgg


Resolution: 1.8→51.16 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1280 5.03 %RANDOM
Rwork0.183 ---
obs0.185 25594 99.5 %-
Displacement parametersBiso mean: 20.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.2458 Å20 Å20 Å2
2--0.2458 Å20 Å2
3----0.4917 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: 1 / Resolution: 1.8→51.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 41 293 1957
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011727HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.012354HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d577SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes326HARMONIC5
X-RAY DIFFRACTIONt_it1727HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4
X-RAY DIFFRACTIONt_other_torsion13.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion221SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2191SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.81 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.1778 -4.71 %
Rwork0.1884 486 -
all0.1879 510 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 24.1921 Å / Origin y: -19.5043 Å / Origin z: -12.8439 Å
111213212223313233
T-0.0558 Å2-0.0066 Å20.0001 Å2--0.0516 Å20.0078 Å2---0.0101 Å2
L0.4879 °2-0.2503 °20.0204 °2-1.3627 °2-0.2019 °2--0.6965 °2
S-0.0123 Å °-0.0007 Å °-0.0252 Å °0.0186 Å °0.0198 Å °-0.0194 Å °0.039 Å °-0.0261 Å °-0.0075 Å °
Refinement TLS groupSelection details: { A|* }

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