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

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Basic information

Entry
Database: PDB / ID: 7ndm
TitleCrystal structure of the heterocyclic toxin methyltransferase from Mycobacterium tuberculosis with bound substrate 4-hydroxyisoquinolin-1(2H)-one
ComponentsHeterocyclic toxin methyltransferase (Rv0560c)
KeywordsTRANSFERASE / Methyltransferase / HQNO-detoxification / SAM-dependent / 1 / 4-dihydroxyisoqunioline
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
MALONATE ION / S-ADENOSYL-L-HOMOCYSTEINE / 4-oxidanyl-2~{H}-isoquinolin-1-one / 2-heptyl-1-hydroxyquinolin-4(1H)-one methyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 2, 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: Heterocyclic toxin methyltransferase (Rv0560c)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1377
Polymers26,4201
Non-polymers7176
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-25 kcal/mol
Surface area9760 Å2
Unit cell
Length a, b, c (Å)70.337, 70.337, 97.885
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 H37Rv / Gene: Rv0560c / Plasmid: pET28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysSRARE / References: UniProt: P9WKL5

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Non-polymers , 5 types, 333 molecules

#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-U8N / 4-oxidanyl-2~{H}-isoquinolin-1-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: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2.3 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.348→60.914 Å / Num. obs: 51446 / % possible obs: 93.3 % / Redundancy: 19.9 % / Biso Wilson estimate: 13.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.084 / Rrim(I) all: 0.273 / Net I/σ(I): 12.1
Reflection shellResolution: 1.348→1.445 Å / Num. unique obs: 2574 / CC1/2: 0.49 / % possible all: 47.9

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Processing

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

7bgg


Resolution: 1.35→19.08 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.057 / SU Rfree Blow DPI: 0.058 / SU Rfree Cruickshank DPI: 0.054
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2574 5.01 %RANDOM
Rwork0.166 ---
obs0.167 51416 82.5 %-
Displacement parametersBiso mean: 16.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.3013 Å20 Å20 Å2
2---0.3013 Å20 Å2
3---0.6026 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: 1 / Resolution: 1.35→19.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1625 0 48 327 2000
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011765HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.052412HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d602SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes341HARMONIC5
X-RAY DIFFRACTIONt_it1765HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.43
X-RAY DIFFRACTIONt_other_torsion13.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion228SEMIHARMONIC5
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_contact2430SEMIHARMONIC4
LS refinement shellResolution: 1.35→1.4 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2525 -6.41 %
Rwork0.2123 963 -
all0.2148 1029 -
obs--14.66 %
Refinement TLS params.Method: refined / Origin x: 24.7836 Å / Origin y: -19.4341 Å / Origin z: -12.9593 Å
111213212223313233
T-0.0244 Å2-0.0008 Å20.0052 Å2--0.0229 Å20.0028 Å2---0.0174 Å2
L0.4134 °20.0903 °2-0.0212 °2-0.7699 °2-0.293 °2--0.5927 °2
S0.0088 Å °0.0246 Å °0.0111 Å °-0.0164 Å °-0.0228 Å °-0.0232 Å °0.0153 Å °-0.0106 Å °0.014 Å °
Refinement TLS groupSelection details: { A|* }

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