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- PDB-6or2: MmpL3 is a lipid transporter that binds trehalose monomycolate an... -

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Basic information

Entry
Database: PDB / ID: 6or2
TitleMmpL3 is a lipid transporter that binds trehalose monomycolate and phosphatidylethanolamine
ComponentsMembrane protein, MmpL family proteinBiological membrane
KeywordsMEMBRANE PROTEIN / transporter
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 / cardiolipin binding / cell septum / phosphatidylethanolamine binding / phospholipid transport / regulation of membrane potential / phosphatidylinositol binding / 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
Chem-L9Q / Trehalose monomycolate exporter MmpL3
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
AuthorsSu, C.-C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: MmpL3 is a lipid transporter that binds trehalose monomycolate and phosphatidylethanolamine.
Authors: Su, C.C. / Klenotic, P.A. / Bolla, J.R. / Purdy, G.E. / Robinson, C.V. / Yu, E.W.
History
DepositionApr 29, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionMay 29, 2019ID: 6N3T
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane protein, MmpL family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6993
Polymers85,4421
Non-polymers1,2572
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.814, 129.457, 154.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Membrane protein, MmpL family protein / Biological membrane / MmpL3


Mass: 85442.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0250 / Variant: ATCC 700084 / mc(2)155 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QP27
#2: Chemical ChemComp-L9Q / (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-stearoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine


Mass: 746.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H80NO8P
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 4.73 Å3/Da / Density % sol: 74.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 30% PEG400, 0.05M Mg(Ac)2, 0.1M NaAc(5.0), and 3% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.56→100 Å / Num. obs: 51822 / % possible obs: 97.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.045 / Rrim(I) all: 0.093 / Χ2: 0.985 / Net I/σ(I): 5.6 / Num. measured all: 206933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.56-2.653.52.23750180.111.312.6141.01296.3
2.65-2.764.11.8951520.2111.0362.1720.97398.2
2.76-2.884.11.3252280.460.7221.5150.96699.5
2.88-3.0440.81251680.6480.450.9350.93998.5
3.04-3.233.90.49452380.830.2740.5690.97598.8
3.23-3.474.10.28452160.940.1530.3251.01499.2
3.47-3.823.90.14551690.9830.080.1671.04597.3
3.82-4.384.20.0852180.9940.0410.090.99297.7
4.38-5.5240.05351640.9970.0280.0610.95996
5.52-1004.10.03652510.9950.020.0420.98393.2

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Processing

Software
NameVersionClassification
PHENIX(dev_3318: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.59→99.252 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2896 3506 3.87 %
Rwork0.2492 --
obs0.2507 90546 92.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→99.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5581 0 85 11 5677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025785
X-RAY DIFFRACTIONf_angle_d0.5237857
X-RAY DIFFRACTIONf_dihedral_angle_d14.5643464
X-RAY DIFFRACTIONf_chiral_restr0.038938
X-RAY DIFFRACTIONf_plane_restr0.004982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.62550.46691150.44522809X-RAY DIFFRACTION76
2.6255-2.6630.40641110.45152953X-RAY DIFFRACTION79
2.663-2.70280.4661310.43023282X-RAY DIFFRACTION88
2.7028-2.7450.41111320.40193359X-RAY DIFFRACTION89
2.745-2.790.34371370.38213548X-RAY DIFFRACTION94
2.79-2.83810.40591450.38313551X-RAY DIFFRACTION95
2.8381-2.88970.36441410.36563602X-RAY DIFFRACTION95
2.8897-2.94530.37931480.3563564X-RAY DIFFRACTION96
2.9453-3.00540.37271480.35543590X-RAY DIFFRACTION94
3.0054-3.07080.35791420.33693442X-RAY DIFFRACTION93
3.0708-3.14220.33821450.32273610X-RAY DIFFRACTION96
3.1422-3.22080.37031480.31393643X-RAY DIFFRACTION97
3.2208-3.30790.35791500.29813607X-RAY DIFFRACTION97
3.3079-3.40520.30291460.2743606X-RAY DIFFRACTION96
3.4052-3.51520.31691490.26813630X-RAY DIFFRACTION96
3.5152-3.64080.35021470.25113569X-RAY DIFFRACTION95
3.6408-3.78660.23771350.22893435X-RAY DIFFRACTION92
3.7866-3.95890.24791470.21533583X-RAY DIFFRACTION96
3.9589-4.16760.24641470.21343635X-RAY DIFFRACTION96
4.1676-4.42880.23581460.20013576X-RAY DIFFRACTION96
4.4288-4.77070.24191400.18763524X-RAY DIFFRACTION94
4.7707-5.25080.22831440.19053492X-RAY DIFFRACTION93
5.2508-6.01050.27671410.23793551X-RAY DIFFRACTION95
6.0105-7.57220.27671350.24813438X-RAY DIFFRACTION92
7.5722-99.32490.29451360.23733441X-RAY DIFFRACTION92
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)
11.2754-1.0402-0.65722.90951.84.5330.0302-0.00080.0573-0.4234-0.28590.1893-0.3718-0.5750.30610.97810.01050.02170.71980.05720.6637134.221473.66255.2477
22.26570.57330.10421.88680.74674.37820.00840.03270.02510.3934-0.02160.15680.81-0.00460.19990.8491-0.04870.05230.41250.03280.6567139.112953.439432.0505
36.8542.4974-2.65463.1583-1.29592.918-0.57661.8924-0.1998-1.67810.93540.63170.3402-1.4829-0.14121.6891-0.1845-0.17751.176-0.25840.8933131.595655.251912.2247
41.1746-0.3479-0.62541.51990.52975.15890.3472-0.37870.36310.0032-0.0201-0.5003-1.48070.4836-0.30530.9724-0.12840.07180.620.01170.7601154.492484.867351.7131
51.39091.12420.52174.23573.19916.1524-0.1752-0.39870.0361-0.20730.4625-0.7-1.0551.4035-0.30560.5848-0.0005-0.00310.90540.04050.6017160.472574.159551.3051
62.1226-0.7247-1.62451.98841.55157.89490.01920.22890.0129-0.3943-0.1152-0.0086-0.7906-0.04510.07870.6625-0.0576-0.11790.51860.02210.533147.222263.264221.3636
70.0306-0.06970.09260.1587-0.21080.28010.15811.0372-1.17670.1803-0.1987-0.69330.94370.7011-0.00212.62350.80530.30551.5734-0.43391.6751136.564434.86168.3098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 207 )
2X-RAY DIFFRACTION2chain 'A' and (resid 208 through 330 )
3X-RAY DIFFRACTION3chain 'A' and (resid 331 through 400 )
4X-RAY DIFFRACTION4chain 'A' and (resid 401 through 501 )
5X-RAY DIFFRACTION5chain 'A' and (resid 502 through 582 )
6X-RAY DIFFRACTION6chain 'A' and (resid 583 through 757 )
7X-RAY DIFFRACTION7chain 'A' and (resid 758 through 761 )

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