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- PDB-3ha7: Crystal structure of HMA (MMAA4) from mycobacterium tuberculosis ... -

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Basic information

Entry
Database: PDB / ID: 3ha7
TitleCrystal structure of HMA (MMAA4) from mycobacterium tuberculosis complexed with S-adenosyl-N-decyl-aminoethyl (SADAE)
ComponentsMETHOXY MYCOLIC ACID SYNTHASE 4
KeywordsTRANSFERASE / S-ADENOSYLMETHIONINE-DEPENDENT METHYLTRANSFERASE FOLD / Methyltransferase
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 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-S-[2-(decylamino)ethyl]-5'-thioadenosine / Hydroxymycolate synthase MmaA4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsVaubourgeix, J. / Boissier, F. / Julien, S. / Mourey, L.
CitationJournal: To be Published
Title: SADAE, a potent bisubstrate inhibitor of mycobacterium tuberculosis mycolic acid methyltransferases
Authors: Vaubourgeix, J. / Bardou, F. / Boissier, F. / Julien, S. / Constant, P. / Ploux, O. / Daffe, M. / Quemard, A. / Mourey, L.
History
DepositionMay 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHOXY MYCOLIC ACID SYNTHASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9882
Polymers36,5211
Non-polymers4671
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.429, 57.429, 205.079
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-313-

HOH

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Components

#1: Protein METHOXY MYCOLIC ACID SYNTHASE 4 / MMAA4 (METHYL MYCOLIC ACID SYNTHASE 4) (MMA4) (HYDROXY MYCOLIC ACID SYNTHASE)


Mass: 36521.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: mmaA4, MMAA4 (RV0642C), Rv0642c / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: Q79FX8, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-B32 / 5'-S-[2-(decylamino)ethyl]-5'-thioadenosine / S-adenosyl-N-decyl-aminoethyl (SADAE)


Mass: 466.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H38N6O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 4-28% PEG 3350, pH 5-9, VAPOR DIFFUSION, HANGING DROP, temperature 285K
PH range: 5-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2007
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.35→18.96 Å / Num. all: 16765 / Num. obs: 16765 / % possible obs: 98.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 60.2 Å2 / Rsym value: 0.046 / Net I/σ(I): 10.1
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2422 / Rsym value: 0.327 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2FK8

2fk8


Resolution: 2.35→18.96 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / SU B: 15.335 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24297 849 5.1 %RANDOM
Rwork0.21097 ---
obs0.21251 15905 97.79 %-
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: 76.932 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å20 Å2
2--1.18 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.35→18.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 32 45 2158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222167
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.972939
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9975267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40823.43896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08915326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6541513
X-RAY DIFFRACTIONr_chiral_restr0.1060.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021653
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.2948
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21542
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3790.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6451.51390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07922143
X-RAY DIFFRACTIONr_scbond_it1.7643907
X-RAY DIFFRACTIONr_scangle_it2.5994.5796
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 68 -
Rwork0.236 1139 -
obs--98.77 %
Refinement TLS params.Method: refined / Origin x: -32.2881 Å / Origin y: 5.9566 Å / Origin z: 16.9297 Å
111213212223313233
T-0.1571 Å20.0648 Å2-0.0352 Å2--0.1799 Å2-0.0016 Å2---0.2201 Å2
L3.1581 °2-1.5419 °20.3698 °2-4.1303 °2-0.7764 °2--5.0745 °2
S-0.2006 Å °0.1831 Å °0.4496 Å °0.0792 Å °0.1888 Å °-0.2439 Å °-0.4334 Å °-0.1045 Å °0.0119 Å °

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