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- PDB-7q2c: mycolic acid methyltransferase Hma (MmaA4) from Mycobac-terium tu... -

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Basic information

Entry
Database: PDB / ID: 7q2c
Titlemycolic acid methyltransferase Hma (MmaA4) from Mycobac-terium tuberculosis in complex with ZT260
ComponentsHydroxymycolate synthase MmaA4
KeywordsTRANSFERASE / mycolic acid methyltransferase mycobacterium tuberculosis fragment based ligand discovery
Function / homology
Function and homology information


mycolic acid biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / peptidoglycan-based cell wall / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / plasma membrane
Similarity search - Function
: / Mycolic acid cyclopropane synthase / : / Mycolic acid cyclopropane synthetase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
6-methyl-2H-chromen-2-one / Hydroxymycolate synthase MmaA4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsMaveyraud, L. / Galy, R. / Mourey, L.
Funding support France, 2items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
Universite de Toulouse France
CitationJournal: Pharmaceuticals / Year: 2021
Title: Fragment-Based Ligand Discovery Applied to the Mycolic Acid Methyltransferase Hma (MmaA4) from Mycobacterium tuberculosis : A Crystallographic and Molecular Modelling Study.
Authors: Galy, R. / Ballereau, S. / Genisson, Y. / Mourey, L. / Plaquevent, J.C. / Maveyraud, L.
History
DepositionOct 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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: Hydroxymycolate synthase MmaA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0766
Polymers36,5211
Non-polymers5555
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.111, 57.111, 205.897
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 Hydroxymycolate synthase MmaA4 / Mycolic acid methyltransferase / MA-MT / S-adenosylmethionine-dependent methyltransferase / AdoMet-MT / SAM-MT


Mass: 36521.305 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: mmaA4, hma, mma4, Rv0642c / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q79FX8, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-3AV / 6-methyl-2H-chromen-2-one


Mass: 160.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: BisTris 50 mM, PEG 3350 4% (w/v), pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.85→35.66 Å / Num. obs: 33875 / % possible obs: 98.4 % / Redundancy: 5.11 % / CC1/2: 0.999 / Rrim(I) all: 0.056 / Rsym value: 0.051 / Net I/σ(I): 15.05
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.72 % / Mean I/σ(I) obs: 0.98 / Num. unique obs: 5254 / CC1/2: 0.591 / Rrim(I) all: 1.264 / Rsym value: 1.093 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2FK7

2fk7


Resolution: 1.9→35.69 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.414 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22556 1619 5.1 %RANDOM
Rwork0.17924 ---
obs0.18159 29917 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.022 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å2-0 Å2
3----2.26 Å2
Refinement stepCycle: 1 / Resolution: 1.9→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 36 138 2463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132390
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172187
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.6673234
X-RAY DIFFRACTIONr_angle_other_deg1.2251.5865034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68321.866134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03615398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7451517
X-RAY DIFFRACTIONr_chiral_restr0.0580.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.50817.1981144
X-RAY DIFFRACTIONr_mcbond_other4.48817.181143
X-RAY DIFFRACTIONr_mcangle_it4.88924.8341430
X-RAY DIFFRACTIONr_mcangle_other4.89924.8511431
X-RAY DIFFRACTIONr_scbond_it6.19719.5581246
X-RAY DIFFRACTIONr_scbond_other6.19619.5551246
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.37427.4491805
X-RAY DIFFRACTIONr_long_range_B_refined8.75454.292678
X-RAY DIFFRACTIONr_long_range_B_other8.75554.2892679
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 106 -
Rwork0.383 2103 -
obs--97.4 %
Refinement TLS params.Method: refined / Origin x: 25.9261 Å / Origin y: 7.9267 Å / Origin z: 16.6765 Å
111213212223313233
T0.1456 Å20.0455 Å20.0079 Å2-0.0887 Å2-0.0021 Å2--0.0155 Å2
L1.268 °2-0.0447 °2-0.638 °2-2.8764 °2-0.3974 °2--2.4372 °2
S-0.1183 Å °0.1254 Å °0.0846 Å °-0.0323 Å °0.2532 Å °-0.0765 Å °-0.4019 Å °-0.2377 Å °-0.1349 Å °

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