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- PDB-7c2m: Crystal structure of mycolic acid transporter MmpL3 from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 7c2m
TitleCrystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with NITD-349
ComponentsChimera of drug exporters of the RND superfamily-like protein and Endolysin
KeywordsMEMBRANE 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 / cardiolipin binding / cell septum / phosphatidylethanolamine binding / phospholipid transport / viral release from host cell by cytolysis / regulation of membrane potential / phosphatidylinositol binding / peptidoglycan catabolic process / cell wall organization / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / response to xenobiotic stimulus / response to antibiotic / plasma membrane
Similarity search - Function
Membrane transport protein MMPL domain / MMPL family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-FFU / Chem-L6T / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / Endolysin / Trehalose monomycolate exporter MmpL3 / Trehalose monomycolate exporter MmpL3
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Enterobacteria phage RB59 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsZhang, B. / Yang, X. / Hu, T. / Rao, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
Chinese Academy of Sciences2017YFC0840300 China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Basis for the Inhibition of Mycobacterial MmpL3 by NITD-349 and SPIRO.
Authors: Yang, X. / Hu, T. / Yang, X. / Xu, W. / Yang, H. / Guddat, L.W. / Zhang, B. / Rao, Z.
History
DepositionMay 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Chimera of drug exporters of the RND superfamily-like protein and Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2469
Polymers103,0071
Non-polymers3,2408
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-0 kcal/mol
Surface area39710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.243, 143.625, 143.198
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chimera of drug exporters of the RND superfamily-like protein and Endolysin / Lysis protein / Lysozyme / Muramidase


Mass: 103006.500 Da / Num. of mol.: 1 / Mutation: C803T,C846A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria), (gene. exp.) Enterobacteria phage RB59 (virus)
Strain: MC2 155 / Gene: mmpL3, MSMEI_0243, e, RB59_126 / Plasmid: pM261
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7G2R2, UniProt: A0A097J809, UniProt: A0QP27*PLUS, lysozyme
#2: Chemical ChemComp-FFU / N-(4,4-dimethylcyclohexyl)-4,6-bis(fluoranyl)-1H-indole-2-carboxamide


Mass: 306.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20F2N2O
#3: Sugar
ChemComp-L6T / alpha-D-glucopyranosyl 6-O-dodecyl-alpha-D-glucopyranoside


Type: saccharideCarbohydrate / Mass: 510.615 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C24H46O11
#4: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID / ADA (buffer)


Mass: 190.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM
Has ligand of interestN

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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: 4.54 Å3/Da / Density % sol: 72.91 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 15% (v/v) polyethylene glycol monomethyl ether 350 (PEGMME 350), 50 mM ADA (N-(2-Acetamido) iminodiacetic acid) (pH 6.5) and 10% (v/v) polyethylene glycol 2000 (PEG2000), protein ...Details: 15% (v/v) polyethylene glycol monomethyl ether 350 (PEGMME 350), 50 mM ADA (N-(2-Acetamido) iminodiacetic acid) (pH 6.5) and 10% (v/v) polyethylene glycol 2000 (PEG2000), protein concentration 5mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.1→45.4 Å / Num. obs: 33226 / % possible obs: 99 % / Redundancy: 13.159 % / Biso Wilson estimate: 95.161 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.116 / Rrim(I) all: 0.121 / Χ2: 1.038 / Net I/σ(I): 17.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.1812.3081.7721.5329638245924080.6571.84997.9
3.18-3.2613.8151.4612.0832768237223720.7851.517100
3.26-3.3613.9311.0882.8332152230823080.8911.129100
3.36-3.4613.8650.823.730920223122300.9230.851100
3.46-3.5813.7480.6894.4230328220722060.9550.716100
3.58-3.712.920.4237.4825129209519450.9750.44192.8
3.7-3.8413.4590.4237.4625963203519290.9790.4494.8
3.84-412.8210.25511.225476198819870.990.26699.9
4-4.1812.4490.18914.0123479188618860.9930.198100
4.18-4.3813.7890.14718.3724820180018000.9970.152100
4.38-4.6213.9010.12222.1924341175117510.9980.127100
4.62-4.913.6990.09527.6622152161716170.9980.098100
4.9-5.2313.4450.09127.4420921155615560.9980.095100
5.23-5.6512.930.10225.0818541143414340.9980.106100
5.65-6.1911.7410.09226.0615721133913390.9970.096100
6.19-6.9213.2790.07134.2716067121012100.9990.074100
6.92-813.0530.04547.44143061096109610.047100
8-9.7912.2120.03263.281122391991910.033100
9.79-13.8510.7440.02766.71797274274210.028100
13.85-45.410.4610.02569.48444643942510.02796.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AJH

6ajh


Resolution: 3.1→45.4 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.66
RfactorNum. reflection% reflection
Rfree0.2813 1994 6 %
Rwork0.2531 --
obs0.2548 33226 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 217.3 Å2 / Biso mean: 103.7535 Å2 / Biso min: 46.17 Å2
Refinement stepCycle: final / Resolution: 3.1→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6952 0 223 0 7175
Biso mean--124.54 --
Num. residues----900
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.180.41841430.393722102353100
3.18-3.260.39121360.342122012337100
3.26-3.360.34191430.312922072350100
3.36-3.470.30691400.274421932333100
3.47-3.590.31811420.281622152357100
3.59-3.740.41511340.38712114224895
3.74-3.910.30951420.261422062348100
3.91-4.110.31031440.227522302374100
4.11-4.370.21881440.210222162360100
4.37-4.710.23921420.208322252367100
4.71-5.180.23491470.198722542401100
5.18-5.930.25911410.234122682409100
5.93-7.460.25121420.245622902432100
7.46-45.40.27291540.255624032557100

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