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

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Basic information

Entry
Database: PDB / ID: 7bgg
TitleCrystal structure of the heterocyclic toxin methyltransferase from Mycobacterium tuberculosis
Componentsheterocyclic toxin methyltransferase (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 / 2-heptyl-1-hydroxyquinolin-4(1H)-one methyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 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
DepositionJan 7, 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 / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: heterocyclic toxin methyltransferase (Rv0560c)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8514
Polymers26,4201
Non-polymers4303
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-17 kcal/mol
Surface area9980 Å2
Unit cell
Length a, b, c (Å)70.235, 70.235, 96.449
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 heterocyclic toxin methyltransferase (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-heptyl-1-hydroxyquinolin-4(1H)-one methyltransferase
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2 M sodium malonate / PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.036→60.825 Å / Num. obs: 131923 / % possible obs: 96.2 % / Observed criterion σ(I): 0.65 / Redundancy: 18.1 % / Biso Wilson estimate: 10.2 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.07951 / Rpim(I) all: 0.0187 / Rrim(I) all: 0.08173 / Net I/σ(I): 18.95
Reflection shellResolution: 1.04→1.099 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.554 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2592 / CC1/2: 0.248 / CC star: 0.63 / Rrim(I) all: 1.607 / % possible all: 67.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nec

4nec


Resolution: 1.04→15.02 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.966 / SU R Cruickshank DPI: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.031 / SU Rfree Blow DPI: 0.031 / SU Rfree Cruickshank DPI: 0.028
RfactorNum. reflection% reflectionSelection details
Rfree0.181 5381 4.99 %RANDOM
Rwork0.175 ---
obs0.175 107798 80.7 %-
Displacement parametersBiso mean: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.1439 Å20 Å20 Å2
2---0.1439 Å20 Å2
3---0.2878 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: 1 / Resolution: 1.04→15.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 28 375 2035
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011765HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.082413HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d608SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes327HARMONIC5
X-RAY DIFFRACTIONt_it1765HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion5.03
X-RAY DIFFRACTIONt_other_torsion13.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion230SEMIHARMONIC5
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_contact2440SEMIHARMONIC4
LS refinement shellResolution: 1.04→1.07 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2391 -4.55 %
Rwork0.2314 2058 -
all0.2317 2156 -
obs--16.32 %
Refinement TLS params.Method: refined / Origin x: 24.3863 Å / Origin y: -19.669 Å / Origin z: -12.8013 Å
111213212223313233
T-0.0251 Å20.0017 Å20.014 Å2--0.0319 Å20.0027 Å2---0.0202 Å2
L0.4835 °20.2131 °2-0.0364 °2-1.0526 °2-0.503 °2--0.6305 °2
S-0.0251 Å °0.0081 Å °-0.0222 Å °-0.0588 Å °-0.0147 Å °-0.0629 Å °0.0476 Å °-0.0104 Å °0.0398 Å °
Refinement TLS groupSelection details: { A|* }

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