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Yorodumi- PDB-7c2n: Crystal structure of mycolic acid transporter MmpL3 from Mycobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c2n | |||||||||
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Title | Crystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with SPIRO | |||||||||
Components | Drug exporters of the RND superfamily-like protein,Endolysin | |||||||||
Keywords | MEMBRANE 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 | |||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) Enterobacteria phage RB59 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å | |||||||||
Authors | Zhang, B. / Yang, X. / Hu, T. / Rao, Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c2n.cif.gz | 194.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c2n.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 7c2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/7c2n ftp://data.pdbj.org/pub/pdb/validation_reports/c2/7c2n | HTTPS FTP |
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-Related structure data
Related structure data | 7c2mC 6ajhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | ||||||
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#2: Sugar | ChemComp-L6T / #3: Chemical | #4: Chemical | ChemComp-FG0 / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.46 Å3/Da / Density % sol: 72.43 % |
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Crystal grow | Temperature: 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 12.5% (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 12.5% (v/v) polyethylene glycol 2000 (PEG2000), protein concentration 5mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.978 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.82→44.54 Å / Num. obs: 43256 / % possible obs: 99.4 % / Redundancy: 5.422 % / Biso Wilson estimate: 81.978 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.085 / Χ2: 1.057 / Net I/σ(I): 15.18 / Num. measured all: 234546 / Scaling rejects: 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AJH Resolution: 2.82→44.54 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 204.09 Å2 / Biso mean: 88.3065 Å2 / Biso min: 36.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.82→44.54 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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