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

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Basic information

Entry
Database: PDB / ID: 8raq
TitleCrystal structure of Mycobacterium tuberculosis MmaA1 with S-adenosyl methionine (SAM)
ComponentsMycolic acid methyltransferase MmaA1
KeywordsTRANSFERASE / methyltransferase / enzyme / fatty acid / bacterium / pathogen
Function / homology
Function and homology information


mycolic acid biosynthetic process / cis-trans isomerase activity / 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-ADENOSYLMETHIONINE / Mycolic acid methyltransferase MmaA1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChaudhary, B. / Kobakhidze, G. / Wachelder, L. / 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 1, 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
A0A0: Mycolic acid methyltransferase MmaA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,90311
Polymers66,6512
Non-polymers1,2529
Water14,880826
1
A: Mycolic acid methyltransferase MmaA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9636
Polymers33,3261
Non-polymers6385
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A0A0: Mycolic acid methyltransferase MmaA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9405
Polymers33,3261
Non-polymers6154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.384, 74.734, 96.773
Angle α, β, γ (deg.)90.000, 90.740, 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

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Protein , 1 types, 2 molecules AA0A0

#1: Protein Mycolic acid methyltransferase MmaA1


Mass: 33325.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: mmaA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WPB1

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Non-polymers , 5 types, 835 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.25 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1M sodium cacodylate trihydrate (pH 6.5), 30% (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: ID30B / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. obs: 115716 / % possible obs: 99.76 % / Redundancy: 4.3 % / Biso Wilson estimate: 17.29 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.041 / Rrim(I) all: 0.088 / Net I/σ(I): 9.6
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.095 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 11519 / CC1/2: 0.6 / CC star: 0.866 / Rpim(I) all: 0.599 / Rrim(I) all: 1.253 / % possible all: 99.74

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.20.1-4487-000refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→19.94 Å / SU ML: 0.1438 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.4834
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1713 2000 1.73 %
Rwork0.1497 113716 -
obs0.15 115716 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.29 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 83 826 5333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01094610
X-RAY DIFFRACTIONf_angle_d1.12226234
X-RAY DIFFRACTIONf_chiral_restr0.0855668
X-RAY DIFFRACTIONf_plane_restr0.01810
X-RAY DIFFRACTIONf_dihedral_angle_d6.0293620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.3491410.29997976X-RAY DIFFRACTION98.11
1.43-1.470.31411430.26598172X-RAY DIFFRACTION99.93
1.47-1.520.2641430.23278042X-RAY DIFFRACTION99.96
1.52-1.560.22981450.21898104X-RAY DIFFRACTION99.3
1.56-1.620.22121350.18638010X-RAY DIFFRACTION98.79
1.62-1.680.20731490.16728144X-RAY DIFFRACTION99.94
1.68-1.760.18121410.1578136X-RAY DIFFRACTION99.98
1.76-1.850.16461440.15168150X-RAY DIFFRACTION99.94
1.85-1.970.17421430.14528144X-RAY DIFFRACTION99.62
1.97-2.120.16741440.13758110X-RAY DIFFRACTION99.89
2.12-2.340.1551400.13238169X-RAY DIFFRACTION99.88
2.34-2.670.16071440.13378170X-RAY DIFFRACTION99.83
2.67-3.360.15641450.14048147X-RAY DIFFRACTION99.33
3.36-19.940.14761430.13658242X-RAY DIFFRACTION99.07
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)
12.20029530984-1.15330852965-0.03585200093591.290146938390.6668832297111.48218086450.0948892979620.0530577780751-0.13308960681-0.0746471494747-0.1246569134410.124704852645-0.133511429044-0.09615704423030.01124443506690.1551733720720.00304578213468-0.01848352465760.145153030126-0.009920797290880.15576323569117.3524274116-29.0795767454-39.4897085826
21.45813278605-0.837507866418-0.05399120640792.99254519220.4669910758331.390891015070.03722436940620.08934264860060.128946983863-0.2252079126440.0389481440958-0.196760214327-0.2658922794060.13566607013-0.06020043936110.184445661789-0.03479082234290.01061292910290.174665595738-0.002700094992120.15206380908833.8053916801-29.4465395737-45.5308095685
30.26073754778-0.00978178572374-0.05339329613730.9317720193790.5727477819641.360767610930.006332566158190.0332195036064-0.0509473373185-0.113599789778-0.06372205367190.0652644694018-0.0259325206991-0.0685930790450.0643254455880.118817022551-0.00254149812259-0.02058904888090.142498987324-0.0180631572620.14278239821622.3751389718-44.0006492249-47.0216276139
41.093034484790.1149062075420.390115124151.403486214160.1317930769551.945651550250.0116139392208-0.0671698223865-0.1612769575030.0818142423293-0.01574184435510.02120866731620.1803919604520.03974521818360.005760847980860.1361832626730.0021568786799-0.002274194612560.142791677640.01186578578970.17310548222131.1473459816-48.656077382-35.2820387443
51.907701947780.882443880507-0.221475806243.049466634990.5667888239083.788666706230.0644585122621-0.0743795408519-0.2486079422940.0102309748860.201934503127-0.4444816050010.3190868724130.00674635993888-0.2084153192930.225100297166-0.0107528677355-0.01835841209040.222330411803-0.04414611657260.22211474102740.1192273283-30.2619434188-16.7851005022
61.82541680969-1.48587690953-0.8786252542272.210159419430.7141215231460.535112050757-0.15567759647-0.274018401665-0.1693591506420.1285070164720.1656682008130.2903576771390.119184444359-0.014073218479-0.01958164618360.211421489264-0.0203822536053-0.02027219913860.2722530778750.03788724046890.19783890479123.8281634139-31.3258080698-19.8931869889
70.820651015899-0.479786081095-0.152947581740.9836668211160.1248118447180.291200419564-0.0143529005272-0.1075410894630.01036664708580.0720910215690.0384750924141-0.07028799155-0.01763278739560.0574999779197-0.02971700548280.131477664031-0.00989661211689-0.02250948264090.160410605939-0.005190383443740.12441717493928.46303503-30.0398219438-31.5552949377
83.26540462930.311356109666-1.238537295832.488533765090.6699643485591.445764011840.0550774652414-0.006959983978380.0858426249585-0.3029184470030.136823193019-0.389372449946-0.1749794372770.142977722241-0.1243215524530.25761324912-0.04288589685960.08979153947930.199238826845-0.05872451928880.22936517034322.30528082710.397149833785-21.1721202975
91.52733693448-0.658181339262-1.100441039682.020308630971.095210272262.953246683480.1253890383260.2899323997690.0928691847409-0.661128162755-0.1249468731570.0148842652478-0.325271531597-0.2090455415530.01080594438770.3196330150920.02672468824760.007481639142240.218267221108-0.003015085778780.1678962520356.133156235376.65649483094-24.3272580283
101.23560821252-0.146220106084-0.3284293516861.602600016410.2723064154561.042696737780.06943796711720.06412310562040.16910618987-0.227146962160.0918003862787-0.204203309199-0.2236519343740.0655301719193-0.1511469870220.239564906281-0.03850237940310.07494647702860.161268080033-0.0317007915350.2048534169116.814829767513.7834002567-13.1872545325
111.36108362311-0.0180348292612-0.4978637456650.4104188574920.5181314851080.8220265980940.111590735514-0.1444200408960.2163469026840.09949693414570.0914592719305-0.221720012711-0.2675146874220.230609662729-0.1952720598840.235642886959-0.03132570867350.03995975572180.216108334974-0.06859063808340.25068587086716.758544742515.4400587317-3.83812471059
120.9523516556710.0990262658023-0.6996880272631.471558647640.6808377578452.04657477067-0.0934111701611-0.0960446164807-0.08581246282250.2331476904510.0356663411301-0.06586714198290.3218291457870.1452982004080.03801977396350.2158429656690.01087322381060.02063827018570.167447766083-0.0159808445770.1762269254298.988183817183.28896422727-1.12636380904
130.08441643829560.246528874780.08715704320630.6876784154070.2835747059770.2273135921520.0027819548157-0.03525024093360.001311390826640.008073844300510.017787454052-0.0195530319712-0.00113195932716-0.0431553678185-0.0165268456790.215445174604-0.01109434195030.03386726597550.195860297834-0.007670002870290.1901281879440.684309731313-6.73518099061-8.82256159078
142.72453043878-1.14739006281-0.9454760786571.92732052580.6695888439881.64459536144-0.0601360169956-0.360312069447-0.0623465889230.3481339683780.08070188769110.0170094762602-0.09404418838640.4580441415690.004368795089130.279480907074-0.006685529895430.01106901571020.2878130921160.02321999550730.18466011646514.6281532991-15.8194603587-10.796691577
150.670939398044-0.499909961086-0.262583065011.773986947961.204282251281.24957727351-0.007058560024680.0961956960337-0.0432846877954-0.0170284632212-0.06784918268450.102749108710.0113855530722-0.1203201557940.08562247350330.170500523253-0.02614150554860.01277170077370.144451915491-0.007542240536860.149714763749.22096912251-3.37573790118-16.9783563589
160.571107755637-0.322000303282-0.5129135865291.037741889580.7819300100450.899615912799-0.0467419969138-0.0608175587068-0.03124777267830.07598213418340.04285904752850.02665521129190.05196803765670.0487024987660.01392140776070.187686673622-0.01512769452020.01267257691320.183298124825-0.01052725145740.16453809401912.5592823285-9.07195603355-17.7152133553
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsLabel asym-IDLabel seq-ID
1X-RAY DIFFRACTION1{ A|16-34 }A1 - 19
2X-RAY DIFFRACTION2{ A|35-59 }A20 - 44
3X-RAY DIFFRACTION3{ A|60-124 }A45 - 109
4X-RAY DIFFRACTION4{ A|125-170 }A110 - 155
5X-RAY DIFFRACTION5{ A|171-184 }A156 - 169
6X-RAY DIFFRACTION6{ A|185-206 }A170 - 191
7X-RAY DIFFRACTION7{ A|207-286 }A192 - 271
8X-RAY DIFFRACTION8{ A0A0|16-34 }H1 - 19
9X-RAY DIFFRACTION9{ A0A0|35-59 }H20 - 44
10X-RAY DIFFRACTION10{ A0A0|60-109 }H45 - 94
11X-RAY DIFFRACTION11{ A0A0|110-130 }H95 - 115
12X-RAY DIFFRACTION12{ A0A0|131-156 }H116 - 141
13X-RAY DIFFRACTION13{ A0A0|157-184 }H142 - 169
14X-RAY DIFFRACTION14{ A0A0|185-206 }H170 - 191
15X-RAY DIFFRACTION15{ A0A0|207-252 }H192 - 237
16X-RAY DIFFRACTION16{ A0A0|253-286 }H238 - 271

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