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- PDB-8rbd: Crystal structure of Mycobacterium tuberculosis MmaA1 with Sinefu... -

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Basic information

Entry
Database: PDB / ID: 8rbd
TitleCrystal structure of Mycobacterium tuberculosis MmaA1 with Sinefungin (SFG)
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
SINEFUNGIN / Mycolic acid methyltransferase MmaA1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._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
A0A0: Mycolic acid methyltransferase MmaA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,44519
Polymers66,6832
Non-polymers1,76217
Water12,755708
1
A: Mycolic acid methyltransferase MmaA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,35011
Polymers33,3421
Non-polymers1,00810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A0A0: Mycolic acid methyltransferase MmaA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0958
Polymers33,3421
Non-polymers7547
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.230, 74.136, 96.774
Angle α, β, γ (deg.)90.000, 90.430, 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-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / 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.: 708 / 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: 44.54 %
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: 1.5→20 Å / Num. obs: 92976 / % possible obs: 99.72 % / Redundancy: 4.6 % / Biso Wilson estimate: 25.01 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.029 / Rrim(I) all: 0.064 / Net I/σ(I): 12.55
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.054 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 8403 / CC1/2: 0.585 / CC star: 0.859 / Rpim(I) all: 0.543 / Rrim(I) all: 1.188 / % possible all: 98.91

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.20.1-4487-000refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1-4487-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.86 Å / SU ML: 0.2406 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2204
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1924 2016 2.17 %
Rwork0.1651 90960 -
obs0.1657 92976 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.17 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4426 0 116 708 5250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00954638
X-RAY DIFFRACTIONf_angle_d0.91696255
X-RAY DIFFRACTIONf_chiral_restr0.0705667
X-RAY DIFFRACTIONf_plane_restr0.0111810
X-RAY DIFFRACTIONf_dihedral_angle_d13.6722628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.45591440.40686479X-RAY DIFFRACTION99.24
1.54-1.580.29621400.32576440X-RAY DIFFRACTION99.73
1.58-1.630.33561450.30126466X-RAY DIFFRACTION99.88
1.63-1.680.31131380.28766445X-RAY DIFFRACTION99.82
1.68-1.740.26881480.23036489X-RAY DIFFRACTION99.88
1.74-1.810.2231450.19016519X-RAY DIFFRACTION99.87
1.81-1.890.19881410.18566454X-RAY DIFFRACTION99.88
1.89-1.990.19931470.17446472X-RAY DIFFRACTION99.83
1.99-2.110.19451440.15526517X-RAY DIFFRACTION99.91
2.11-2.280.1911420.14786496X-RAY DIFFRACTION99.94
2.28-2.510.18031440.14666496X-RAY DIFFRACTION99.88
2.51-2.870.1811470.14926525X-RAY DIFFRACTION99.94
2.87-3.610.16821450.15316549X-RAY DIFFRACTION99.9
3.61-19.860.17431460.14776613X-RAY DIFFRACTION99.46
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)
10.7781958778450.012612557265-0.1575179378161.28576794586-0.2746677919711.246387236660.0194332764919-0.00206085822669-0.08111384304240.0892031481938-0.0516674128323-0.004357125570640.001164739257450.001302795573920.03545081769350.1920128407080.00545485018575-0.02194977627830.2031427999230.009916888703250.20382404825915.2159275555-3.7030609428842.2375475952
23.404588669450.5553463381740.8171582669741.71483054776-0.1819533833331.63214136821-0.1732853008810.449265265497-0.304073408249-0.08907577389130.1880098997410.08430025300640.2202288678760.2552329012990.00202332393380.3402848952690.0525104386676-0.01069322653770.4063193355380.01703200012630.2965504512769.125346432037.9262610116416.8580639621
30.2465390128370.1559372070030.3601025694462.001663325270.008894919670491.033449511350.01612563709620.132682082289-0.103742689422-0.156585336584-0.02094830883910.04262363716480.0183697205565-0.08710002741720.04469333856730.2423844722160.0121721424069-0.04486434898550.312170787903-0.03049678829790.2871961417685.97281843226-4.1941504281929.5528081388
41.088425063720.565451916129-0.3443632615050.849281753805-0.1218388199480.3095475551360.03848350967010.1572640286560.062639350136-0.05138372075950.02711223753120.0103478039619-0.0550298548128-0.0582791908405-0.05140604922240.2511687238620.010113065904-0.02373030968630.2665114821680.02154274200870.22647690624416.88359693812.076539636431.6098518607
50.560392381332-0.0729149888826-0.1288689965491.85877265814-0.6137333714270.873416086337-0.00193126429147-0.02026469200920.08267498351310.1792098708370.1108517900830.163908627632-0.15317193643-0.0478241207398-0.1209142413010.2661946023730.009760307158110.02461030542320.2439414747210.0216018466890.23489583208229.478200572243.488083438711.8283304887
62.170418659860.892891866802-0.6996985258281.12668798153-0.7585854283131.44178604039-0.1151595844070.311244326108-0.162235732159-0.3214848946580.2288068366990.07853974675150.0565663829517-0.484512483709-0.06185210739740.326049538456-0.00497653342168-0.01551004367250.364408033092-0.009828458957510.28953766247426.535658799321.426798533310.7630058993
70.4037541285010.389964834293-0.3289043827561.60878076787-1.084759966121.11854467924-0.0409753274894-0.0415756678516-0.02424706560370.01334870441230.0258682868958-0.05930429662870.03190039126660.01577263374260.01620477784350.2758078969410.02764978694150.0140866613710.2535753737010.01507805533150.23134487665930.701830802131.273478262517.3435933455
Refinement TLS group
IDRefine-IDRefine TLS-IDLabel asym-IDLabel seq-ID
1X-RAY DIFFRACTION1A1 - 155
2X-RAY DIFFRACTION2A156 - 181
3X-RAY DIFFRACTION3A182 - 212
4X-RAY DIFFRACTION4A213 - 271
5X-RAY DIFFRACTION5K1 - 169
6X-RAY DIFFRACTION6K170 - 191
7X-RAY DIFFRACTION7K192 - 271

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