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- PDB-7q2d: mycolic acid methyltransferase Hma (MmaA4) from Mycobac-terium tu... -

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Basic information

Entry
Database: PDB / ID: 7q2d
Titlemycolic acid methyltransferase Hma (MmaA4) from Mycobac-terium tuberculosis in complex with ZT320
ComponentsHydroxymycolate synthase MmaA4
KeywordsTRANSFERASE / mycolic acid methyltransferase mycobacterium tuberculosis fragment based ligand discovery
Function / homology
Function and homology information


cyclopropane-fatty-acyl-phospholipid synthase activity / mycolic acid biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / lipid biosynthetic process / 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
2-METHOXY-5-METHYLANILINE / Hydroxymycolate synthase MmaA4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.89 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)36,9365
Polymers36,5211
Non-polymers4154
Water1,928107
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)57.022, 57.022, 207.345
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-ZZT / 2-METHOXY-5-METHYLANILINE


Mass: 137.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
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: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.9→57.02 Å / Num. obs: 31853 / % possible obs: 100 % / Redundancy: 11.39 % / CC1/2: 0.998 / Rrim(I) all: 0.085 / Rsym value: 0.081 / Net I/σ(I): 16.15
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 11.76 % / Mean I/σ(I) obs: 2.55 / Num. unique obs: 5032 / CC1/2: 0.892 / Rrim(I) all: 0.951 / Rsym value: 0.909 / % possible all: 100

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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: 1.89→49.38 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.195 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22809 1645 5.1 %RANDOM
Rwork0.18557 ---
obs0.18771 30494 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 66.131 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å2-0 Å2
3----1.43 Å2
Refinement stepCycle: 1 / Resolution: 1.89→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 28 107 2420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132389
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182181
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.6573236
X-RAY DIFFRACTIONr_angle_other_deg1.2361.5865011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37721.752137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01815390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5751518
X-RAY DIFFRACTIONr_chiral_restr0.0570.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02583
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_it5.48722.3991153
X-RAY DIFFRACTIONr_mcbond_other5.48222.381152
X-RAY DIFFRACTIONr_mcangle_it5.95632.3231443
X-RAY DIFFRACTIONr_mcangle_other5.95932.3431444
X-RAY DIFFRACTIONr_scbond_it7.13924.7911236
X-RAY DIFFRACTIONr_scbond_other7.13624.8121237
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9234.9161794
X-RAY DIFFRACTIONr_long_range_B_refined9.47969.2972624
X-RAY DIFFRACTIONr_long_range_B_other9.4869.3232625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 106 -
Rwork0.296 2157 -
obs--97.54 %
Refinement TLS params.Method: refined / Origin x: 26.119 Å / Origin y: 8.275 Å / Origin z: 16.762 Å
111213212223313233
T0.1242 Å2-0.0224 Å2-0.0025 Å2-0.0467 Å2-0.0007 Å2--0.0299 Å2
L1.1007 °2-0.174 °2-0.5354 °2-1.9092 °20.159 °2--2.353 °2
S-0.0673 Å °0.0225 Å °0.1753 Å °-0.13 Å °0.179 Å °-0.0809 Å °-0.4069 Å °-0.0709 Å °-0.1118 Å °

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