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- PDB-6n40: Crystal structure of MmpL3 from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 6n40
TitleCrystal structure of MmpL3 from Mycobacterium smegmatis
ComponentsMembrane protein, MmpL family protein
KeywordsMEMBRANE PROTEIN / transporter / ANTIBIOTIC
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 speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.307 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: To be published
Title: Crystal structure of MmpL3 from Mycobacterium smegmatis
Authors: Su, C.-C. / Yu, E.W.
History
DepositionNov 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 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

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Assembly

Deposited unit
A: Membrane protein, MmpL family protein


Theoretical massNumber of molelcules
Total (without water)85,4421
Polymers85,4421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.239, 130.917, 155.633
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


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 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QP27

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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: 5.02 Å3/Da / Density % sol: 75.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 20%PEG400 and 0.1M LiCl

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Data collection

DiffractionMean temperature: 298 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: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→100.185 Å / Num. obs: 26284 / % possible obs: 94 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.054 / Rrim(I) all: 0.155 / Χ2: 1.19 / Net I/σ(I): 5 / Num. measured all: 220075
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.4282.87258925740.5741.0583.0670.95199.8
3.42-3.558.71.88125760.7050.6651.9990.92199.9
3.55-3.728.61.23325850.8010.4391.3110.94399.9
3.72-3.918.50.67825870.9420.2420.7211.03599.9
3.91-4.167.70.4326190.9680.1610.4611.14699.9
4.16-4.488.80.29226110.9850.1040.3111.256100
4.48-4.938.70.18726120.9930.0670.1991.41199.8
4.93-5.648.10.19326350.9890.0710.2071.29599.5
5.64-7.118.80.13826900.9940.0490.1471.26399.9
7.11-1007.80.06127950.9970.0240.0651.66499

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3177: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementResolution: 3.307→100.185 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 43.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3145 1299 4.97 %
Rwork0.2663 --
obs0.2684 26134 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.307→100.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5535 0 0 0 5535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035645
X-RAY DIFFRACTIONf_angle_d0.6317681
X-RAY DIFFRACTIONf_dihedral_angle_d18.2612042
X-RAY DIFFRACTIONf_chiral_restr0.04919
X-RAY DIFFRACTIONf_plane_restr0.005970

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