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- PDB-8rbl: Crystal structure of Mycobacterium tuberculosis MmaA1 with S-aden... -

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Basic information

Entry
Database: PDB / ID: 8rbl
TitleCrystal structure of Mycobacterium tuberculosis MmaA1 with S-adenosyl homocysteine
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
S-ADENOSYL-L-HOMOCYSTEINE / Mycolic acid methyltransferase MmaA1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
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)68,32717
Polymers66,6832
Non-polymers1,64415
Water12,412689
1
A: Mycolic acid methyltransferase MmaA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,31911
Polymers33,3421
Non-polymers97710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mycolic acid methyltransferase MmaA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0086
Polymers33,3421
Non-polymers6675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.235, 74.334, 96.704
Angle α, β, γ (deg.)90.000, 90.230, 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: 33341.543 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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.2 M ammonium sulfate, 0.1M sodium cacodylate trihydrate (pH 6.4), 25% (w/v) polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jan 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. obs: 84555 / % possible obs: 99.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 24.28 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.03 / Rrim(I) all: 0.066 / Net I/σ(I): 12.73
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.189 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 8422 / CC1/2: 0.587 / CC star: 0.86 / Rpim(I) all: 0.639 / Rrim(I) all: 1.355 / % possible all: 98.13

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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: 1.55→19.87 Å / SU ML: 0.1976 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4402
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1992 1999 2.36 %
Rwork0.1724 82556 -
obs0.173 84555 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.58 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4426 0 106 689 5221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714643
X-RAY DIFFRACTIONf_angle_d0.98916267
X-RAY DIFFRACTIONf_chiral_restr0.061667
X-RAY DIFFRACTIONf_plane_restr0.0083813
X-RAY DIFFRACTIONf_dihedral_angle_d12.9284657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.34921400.36935811X-RAY DIFFRACTION98.07
1.59-1.630.33131450.33025823X-RAY DIFFRACTION99.53
1.63-1.680.27021390.28115848X-RAY DIFFRACTION99.78
1.68-1.730.27081430.24635934X-RAY DIFFRACTION99.84
1.73-1.790.24231390.235895X-RAY DIFFRACTION99.82
1.79-1.870.27011440.20465873X-RAY DIFFRACTION99.88
1.87-1.950.22791440.18775897X-RAY DIFFRACTION99.87
1.95-2.050.20931380.17745888X-RAY DIFFRACTION99.92
2.05-2.180.21951430.16695912X-RAY DIFFRACTION99.87
2.18-2.350.19121410.16495875X-RAY DIFFRACTION99.7
2.35-2.590.21771470.16825935X-RAY DIFFRACTION99.97
2.59-2.960.21721430.16855909X-RAY DIFFRACTION99.95
2.96-3.720.16921430.15485954X-RAY DIFFRACTION99.77
3.73-19.870.15681500.14646002X-RAY DIFFRACTION99.71
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)
10.938144223702-0.0224439018275-0.19475964431.42742091418-0.3584801953971.39449923578-0.007635685068060.0066348544668-0.1359730272860.100929243725-0.0146706152638-0.0302955707531-0.008629751718410.0087824508584.70474891997E-50.1584628355260.0081885000354-0.01733383881260.1896610163840.007921823810970.20691051700315.2646351882-3.7837327338642.246016643
20.0951049749948-0.1327495048640.05925653708970.218258826957-0.08290253125460.034605159691-0.2395049837550.696119945217-0.467427919576-0.2775772818260.3040517280880.05365190681530.3416999908670.05583108145860.0002377806953350.3667439379150.007814375361780.008128662288690.4560297059140.03883293402530.3632572478169.397549916487.9889089647717.0132640906
30.0955853631417-0.183794657340.1983716553260.316760596094-0.2138161571890.4587287655530.04663694364850.306724629363-0.139629144133-0.254563845391-0.0589956189318-0.176419189331-0.0208084306733-0.1044134617450.01425193205410.228499974584-0.00807918406736-0.01351828480220.320395539523-0.04892815935870.3563342178376.45731502317-4.0273696273929.3926062322
40.584200198418-0.0652326740615-0.2832961842450.577810395353-0.04760055609970.4106633001910.02230358826030.1696883832590.0178729138942-0.0969196227970.043706792884-0.0311513387826-0.0808066963594-0.0168401506407-0.0001006897518210.2238404189390.00273024461509-0.01261956027190.2378989668370.01598571808710.19275901997617.32963452912.051289126931.7326164582
51.10913414206-0.195569422364-0.365220364191.98921042964-0.6234982115191.33159768944-0.038762186123-0.01613351164520.02626026486630.2151471382140.1144850081770.256394480534-0.137485098909-0.08355716846950.001472374001870.2601441062080.007778772371240.04354385731120.2077989750380.01246677336790.24387902507528.339360996945.807982183611.9675406171
60.182807502736-0.133465161199-0.05154033942270.0831786571731-0.03866259684340.114486004381-0.08777994062180.37288255788-0.418074247622-0.2278116637030.001835605743620.04011997871740.149889472274-0.2682147937730.0003210308169170.295125099391-0.01642848913710.01270878181030.305174015391-0.02411856727550.2641673545435.340818328417.974622876311.3157634483
70.16832741452-0.2366616941560.2849642833680.304643288511-0.3992473369690.470477103513-0.07155609578980.0239539539634-0.239699755704-0.125666426904-0.0771346410621-0.09633437327710.354433527254-0.0129710533749-0.001235579075620.322155176645-0.01705233843650.0762009409330.2685616633880.01074316867240.29138128570738.065083656834.63500083556.23811921471
80.08792164609970.09666100195330.07910084254870.929312754266-0.5940598814710.606764928285-0.03308307100950.0152955725241-0.01131154793360.07861034274890.07832892712530.07633758398460.00339609476369-0.06366986869910.002834824497190.2585285386670.03042247222180.04607256967360.199613285990.02753287921780.19296478188426.576768379429.212663354521.4691903147
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 170 )AA16 - 1701 - 155
22chain 'A' and (resid 171 through 196 )AA171 - 196156 - 181
33chain 'A' and (resid 197 through 227 )AA197 - 227182 - 212
44chain 'A' and (resid 228 through 286 )AA228 - 286213 - 271
55chain 'B' and (resid 16 through 170 )BK16 - 1701 - 155
66chain 'B' and (resid 171 through 196 )BK171 - 196156 - 181
77chain 'B' and (resid 197 through 227 )BK197 - 227182 - 212
88chain 'B' and (resid 228 through 286 )BK228 - 286213 - 271

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