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- PDB-8rbe: Crystal structure of Mycobacterium tuberculosis MmaA1 in apo form -

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Basic information

Entry
Database: PDB / ID: 8rbe
TitleCrystal structure of Mycobacterium tuberculosis MmaA1 in apo form
ComponentsMycolic acid methyltransferase MmaA1
KeywordsTRANSFERASE / methyltransferase / enzyme / fatty acid / bacterium / pathogen
Function / homology
Function and homology information


lipid biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation
Similarity search - Function
: / Mycolic acid cyclopropane synthase / : / Mycolic acid cyclopropane synthetase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Mycolic acid methyltransferase MmaA1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKobakhidze, G. / Wachelder, L. / Chaudhary, B. / Mazumdar, P.A. / Madhurantakam, C. / Dong, G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundI5960-B2 Austria
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2025
Title: Crystal structures of the mycolic acid methyl transferase 1 (MmaA1) from Mycobacterium tuberculosis in the apo-form and in complex with different cofactors reveal unique features for substrate binding.
Authors: Chaudhary, B. / Kobakhidze, G. / Wachelder, L. / Mazumdar, P.A. / Dong, G. / Madhurantakam, C.
History
DepositionDec 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: audit_author / citation / citation_author
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Revision 1.2Jun 4, 2025Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.pdbx_database_id_PubMed ..._audit_author.name / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mycolic acid methyltransferase MmaA1
B: Mycolic acid methyltransferase MmaA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8354
Polymers66,6512
Non-polymers1842
Water11,638646
1
A: Mycolic acid methyltransferase MmaA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4182
Polymers33,3261
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mycolic acid methyltransferase MmaA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4182
Polymers33,3261
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.616, 74.840, 97.595
Angle α, β, γ (deg.)90.000, 91.360, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Mycolic acid methyltransferase MmaA1 / S-adenosylmethionine-dependent methyltransferase / AdoMet-MT / SAM-MT


Mass: 33325.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cmaD, mma1, mmaA1, mmas-1, BQ2027_MB0664C / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A5Q1, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 10% (v/v) 2-propanol 20% (w/v) polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 47320 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 27.09 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.063 / Rrim(I) all: 0.14 / Net I/σ(I): 9.13
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.198 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 4673 / CC1/2: 0.533 / CC star: 0.834 / Rpim(I) all: 0.599 / Rrim(I) all: 1.344 / % possible all: 99.83

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.79 Å / SU ML: 0.2288 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9993
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2022 2005 4.24 %
Rwork0.1738 45315 -
obs0.175 47320 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 12 646 5082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324540
X-RAY DIFFRACTIONf_angle_d0.61736142
X-RAY DIFFRACTIONf_chiral_restr0.0414656
X-RAY DIFFRACTIONf_plane_restr0.0049806
X-RAY DIFFRACTIONf_dihedral_angle_d5.74614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.30241420.26883165X-RAY DIFFRACTION98.75
1.94-20.31191470.27143227X-RAY DIFFRACTION99.82
2-2.060.29781430.2353199X-RAY DIFFRACTION100
2.06-2.120.28391430.21343224X-RAY DIFFRACTION99.91
2.12-2.20.25581450.20293274X-RAY DIFFRACTION99.91
2.2-2.290.25981430.19653180X-RAY DIFFRACTION99.82
2.29-2.390.24071410.1883244X-RAY DIFFRACTION99.91
2.39-2.520.23961420.1843235X-RAY DIFFRACTION99.94
2.52-2.670.22451500.17513251X-RAY DIFFRACTION100
2.67-2.880.21161380.17853225X-RAY DIFFRACTION99.82
2.88-3.170.20541460.1753256X-RAY DIFFRACTION100
3.17-3.620.18461400.15093242X-RAY DIFFRACTION99.85
3.62-4.560.1321390.13573272X-RAY DIFFRACTION99.8
4.56-19.790.16621460.15973321X-RAY DIFFRACTION99.91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7080268205210.0881425895183-0.2098452704040.9561763569640.5209336363681.090217184950.0148011652721-0.0303076021810.03629954223060.060937312047-0.005716527463070.02276713655960.02682057091750.002073217351256.76993929588E-50.1857801559680.0217658500007-0.01049019570390.1932783983460.0003741653039550.2033642830615.21779229873.9357059334740.395356068
21.377946164560.8445059649451.346421600230.5201527754620.8171715300411.33788844832-0.1597998852410.237759714830.3189566257750.1586631338440.3219697345070.553173018946-0.23208142530.1317912585860.1003078027280.2762055756920.07390732073720.07143250118070.3255334890520.07714261900520.3936461073662.08086876503-5.3739191333620.1457017696
30.433245501394-0.0313922644880.1233253219220.8015256044910.1508094048880.491234995993-0.04189255589230.0859975145599-0.0367006201931-0.118594788590.0886278030286-0.03221443302420.01450537201710.0298521968023.73815104444E-50.2106892929910.0111546185624-0.001757070931440.224229354316-0.004281637494750.2131260054296.42752529413-6.2505541601332.1274145429
40.01809904926020.02048503223480.02533724326930.1765292791910.1255088115590.09694833410460.0117383377339-0.0577813146599-0.1469682358760.1069552304880.0310764199626-0.1428562908620.1795365061820.2454921254810.0001899674033680.3040453190170.0194303011613-0.0269610294740.349826050899-0.02108488880450.3092938012120.603250842587-36.829982444721.780116843
50.252637342566-0.2535388191530.1787183246960.7951500373650.2961046855260.5455269775730.0351388165986-0.14862113344-0.09772942130770.2138887123820.0484578801806-0.05169092983130.2025213831140.128167966941-8.46236352547E-50.302838054129-0.00139508907656-0.001895600763210.2996957374610.01088164425230.263971126815-8.38822374262-47.576029409917.1489738971
60.372566637331-0.01327053214720.02513216601240.1524526625980.162902947860.2171907321840.1284372346510.181000560135-0.311289875103-0.1739260538670.0943231409634-0.3105851785460.3464844197880.2136095577070.001935895990850.3606217366530.0313887624309-0.005802423877140.326582527682-0.003201670052740.322779016346-4.26644313308-51.62682631014.03746705583
70.473284011896-0.47501466072-0.2462997051150.4754914019060.249326399280.4207061537360.02539753613250.1090021387520.0462727139136-0.18104843267-0.0283298995683-0.0744470718907-0.03526736425890.009410392731247.2101590613E-50.270156383386-0.01987362385860.0004442104599210.2691021372860.005073841119950.262423038985-16.2851681605-34.26144366485.01525710574
80.4517512271920.5574756347850.04935115121170.8651500751890.08084438451940.0304574202334-0.152009405820.4467791825970.38913220487-0.3617606775110.0333370859660.125219513040.1399976956020.645966755869-0.006123597192930.3564851011110.0430332558909-0.01028864706670.4352926479580.0125144673320.354083427862-6.73487178485-19.969308640711.4144174063
90.40376296017-0.226146612840.02465536442340.6175863784360.6238458318440.826410666354-0.0926140006147-0.09146047945390.155262855677-0.0233433355525-0.0208501180360.0554261121845-0.111369578114-0.0455560912261-0.0001954776274680.2515958819350.00686425540342-0.005613755261440.242341142770.01385874259920.226965339766-10.7003493496-30.355498406217.451967355
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 16 through 184 )AA16 - 1841 - 169
22chain 'A' and (resid 185 through 206 )AA185 - 206170 - 191
33chain 'A' and (resid 207 through 286 )AA207 - 286192 - 271
44chain 'B' and (resid 16 through 34 )BC16 - 341 - 19
55chain 'B' and (resid 35 through 109 )BC35 - 10920 - 94
66chain 'B' and (resid 110 through 130 )BC110 - 13095 - 115
77chain 'B' and (resid 131 through 184 )BC131 - 184116 - 169
88chain 'B' and (resid 185 through 206 )BC185 - 206170 - 191
99chain 'B' and (resid 207 through 286 )BC207 - 286192 - 271

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