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- PDB-9kbe: Crystal structure of mycolic acid transporter MmpL3 from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 9kbe
TitleCrystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with indolcarboxamide
ComponentsTrehalose monomycolate exporter MmpL3
KeywordsMEMBRANE PROTEIN / MEMBRANE PROTEIN TRANSPORTER RND SUPERFAMILY CELL WALL BIOSYNTHESIS ANTITUBERCULAR DRUGS / TRANSPORT PROTEIN
Function / homology
Function and homology information


phosphatidylethanolamine transfer activity / phosphatidylglycerol binding / trehalose transmembrane transporter activity / trehalose transport / mycolate cell wall layer assembly / cell wall biogenesis / diacylglycerol binding / cell pole / cell tip / mycolic acid biosynthetic process ...phosphatidylethanolamine transfer activity / phosphatidylglycerol binding / trehalose transmembrane transporter activity / trehalose transport / mycolate cell wall layer assembly / cell wall biogenesis / diacylglycerol binding / cell pole / cell tip / mycolic acid biosynthetic process / cell septum / phospholipid transport / cardiolipin binding / phosphatidylethanolamine binding / phosphatidylinositol binding / regulation of membrane potential / cell wall organization / response to xenobiotic stimulus / response to antibiotic / plasma membrane
Similarity search - Function
: / Membrane transport protein MMPL domain / MMPL family
Similarity search - Domain/homology
: / Trehalose monomycolate exporter MmpL3
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMurakami, S. / Okada, U. / Yamashita, E. / Pieroni, M. / Carosati, E.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K06099 Japan
Japan Society for the Promotion of Science (JSPS)JP21H02412 Japan
CitationJournal: To Be Published
Title: Crystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with indolcarboxamide.
Authors: Murakami, S.
History
DepositionOct 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trehalose monomycolate exporter MmpL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7908
Polymers85,4421
Non-polymers3,3487
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area31160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.289, 105.340, 89.468
Angle α, β, γ (deg.)90.000, 114.521, 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 Trehalose monomycolate exporter MmpL3 / TMM exporter MmpL3 / MmpL3 transporter / Mycobacterial membrane protein large 3


Mass: 85442.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The six histidine residues at the C-terminal are His-tag for protein purification.
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: mmpL3, MSMEG_0250, MSMEI_0243 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0QP27
#2: Chemical ChemComp-A1L5O / N-cycloheptyl-4,6-dimethyl-1H-indole-2-carboxamide


Mass: 284.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
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: 4.23 Å3/Da / Density % sol: 70.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20mM HEPES pH7.5, 150mM NaCl, 0.05% DDM, 1.17mM Indolecarboxyamide, 2% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2023
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.15→46.94 Å / Num. obs: 77682 / % possible obs: 99.91 % / Redundancy: 25.9 % / Biso Wilson estimate: 58.03 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.024 / Net I/σ(I): 12.4
Reflection shellResolution: 2.15→2.18 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3853 / CC1/2: 0.744 / Rpim(I) all: 0.573 / % possible all: 98.59

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→43.42 Å / SU ML: 0.3014 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.3099
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2424 3855 4.97 %
Rwork0.2158 73698 -
obs0.217 77553 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.22 Å2
Refinement stepCycle: LAST / Resolution: 2.15→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5535 0 231 100 5866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00345884
X-RAY DIFFRACTIONf_angle_d0.56787995
X-RAY DIFFRACTIONf_chiral_restr0.039982
X-RAY DIFFRACTIONf_plane_restr0.005970
X-RAY DIFFRACTIONf_dihedral_angle_d9.5918836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.170.40881360.39322596X-RAY DIFFRACTION97.99
2.17-2.20.44261200.38152626X-RAY DIFFRACTION99.85
2.2-2.230.42121300.35492630X-RAY DIFFRACTION99.93
2.23-2.260.39391280.34362610X-RAY DIFFRACTION99.82
2.26-2.290.33061360.28472651X-RAY DIFFRACTION99.93
2.29-2.330.25451340.26912607X-RAY DIFFRACTION99.75
2.33-2.360.29551190.26672641X-RAY DIFFRACTION99.42
2.36-2.40.30471470.25262629X-RAY DIFFRACTION99.78
2.4-2.440.28311540.25732596X-RAY DIFFRACTION99.78
2.44-2.490.29321460.24052637X-RAY DIFFRACTION99.75
2.49-2.530.29521420.23982591X-RAY DIFFRACTION99.89
2.53-2.590.33071240.2422626X-RAY DIFFRACTION99.75
2.59-2.640.23241400.23422638X-RAY DIFFRACTION99.71
2.64-2.70.27011500.23442621X-RAY DIFFRACTION99.86
2.7-2.770.26841620.22462608X-RAY DIFFRACTION99.71
2.77-2.850.25591470.22382588X-RAY DIFFRACTION99.74
2.85-2.930.28281650.22052616X-RAY DIFFRACTION99.86
2.93-3.020.26431280.21452630X-RAY DIFFRACTION99.82
3.02-3.130.23941390.21862648X-RAY DIFFRACTION99.86
3.13-3.260.3021250.22732628X-RAY DIFFRACTION99.82
3.26-3.410.31561260.23452642X-RAY DIFFRACTION99.89
3.41-3.590.21031470.20952638X-RAY DIFFRACTION99.89
3.59-3.810.21831470.2012634X-RAY DIFFRACTION100
3.81-4.10.25041330.19722653X-RAY DIFFRACTION99.96
4.1-4.520.18131020.18812698X-RAY DIFFRACTION100
4.52-5.170.18421280.18092662X-RAY DIFFRACTION99.96
5.17-6.510.25851400.22222671X-RAY DIFFRACTION100
6.51-43.420.22191600.21162683X-RAY DIFFRACTION99.34
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)
10.552957397343-0.280707067650.6645518324810.7413578574730.2680067239440.726193691982-0.5510397769170.179383692872-0.170001085250.1044530947890.173913561030.1894509961880.9853404471570.0971125574835-0.0007838482977830.735603963590.01336899404590.02380410796790.678467033498-0.02228253467220.597606271839-14.83039671292.78330148343.29738517828
22.27912566473-0.007383412745460.06744601108210.7811964245750.1684664781912.03951559460.04512607723-0.1061486458840.197010743378-0.0403089449205-0.0632013909089-0.300403749886-0.1998882930910.227604686896-6.20145117265E-50.623164838744-0.005823577255630.04200600030170.4815660330290.007872459709260.62403696331312.3793398626.4881561549-32.3364321642
30.098784336031-0.0440665862266-0.2815801495920.250347166720.1530290662980.04215676449940.0704915102315-0.4262345075480.07413779582160.147613106884-0.0131863995697-0.1662691549-0.4659413271790.2327264639490.0001077300781980.6633723841370.05942523188130.03962895429660.7302619035620.00557744250450.648728631578-11.096283998225.4368537195-13.2205358728
40.1071397367790.125612032007-0.4548533693540.53246528923-0.1279569488482.11174790616-0.02388727317240.06457172314070.1103233602230.1019691985940.04141945881550.09404944272310.0923602977059-0.4152568070790.001648261859860.4759353523710.01356014633210.001220437519980.5732678755340.02582795582430.559517633352-21.696832715814.240914083-13.9698648866
51.46588505120.6851101587830.2293659926251.031574003180.6193407833211.83347756237-0.0583637926410.1792948385070.175712556541-0.167286184680.0586973278636-0.03903951572750.110674365149-0.167887759618-1.60672806795E-50.7562366663720.04875700914610.05385245558550.6115306680970.0512531779570.6423154187042.3994050730212.445430146-53.2611376293
60.949269995921-0.2402875020580.08825145375111.718229449040.1963160495811.43780791782-0.122032732190.1724290370830.2601285554560.02847730686580.3149829166790.1987476889580.13474671112-1.006794986380.002091882327150.506721130439-0.079529575396-0.01627056617930.9949837817060.05116901138770.540946398396-31.737278920310.7291371209-21.2895567019
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 36 )1 - 361 - 36
22chain 'A' and (resid 37 through 164 )37 - 16437 - 164
33chain 'A' and (resid 165 through 207 )165 - 207165 - 207
44chain 'A' and (resid 208 through 463 )208 - 463208 - 437
55chain 'A' and (resid 464 through 548 )464 - 548438 - 522
66chain 'A' and (resid 549 through 751 )549 - 751523 - 725

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