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Yorodumi- PDB-6t1z: LmrP from L. lactis, in an outward-open conformation, bound to Ho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t1z | ||||||
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Title | LmrP from L. lactis, in an outward-open conformation, bound to Hoechst 33342 | ||||||
Components | LmrP integral membrane protein | ||||||
Keywords | TRANSPORT PROTEIN / Transmembrane multidrug transporter | ||||||
Function / homology | Function and homology information transmembrane transporter activity / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Hutchin, A. / Debruycker, V. / Masureel, M. / Legrand, P. / Remaut, H. / Govaerts, C. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2020 Title: An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity. Authors: Debruycker, V. / Hutchin, A. / Masureel, M. / Ficici, E. / Martens, C. / Legrand, P. / Stein, R.A. / Mchaourab, H.S. / Faraldo-Gomez, J.D. / Remaut, H. / Govaerts, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t1z.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t1z.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 6t1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/6t1z ftp://data.pdbj.org/pub/pdb/validation_reports/t1/6t1z | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 45277.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Gene: lmrP / Plasmid: lmrp-pHLP5-3C Production host: Lactococcus lactis subsp. cremoris NZ9000 (lactic acid bacteria) References: UniProt: Q48658 |
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#4: Sugar |
-Non-polymers , 4 types, 7 molecules
#2: Chemical | ChemComp-HT1 / | ||||
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#3: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.68 Å3/Da / Density % sol: 73.74 % / Description: Thin plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 80 mM SPG pH 7, 20% (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97166 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2014 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97166 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Entry-ID: 6T1Z / CC1/2: 1
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Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: In-house structure Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 7.664 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 2.169 / SU Rfree Blow DPI: 0.382 / SU Rfree Cruickshank DPI: 0.394
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Displacement parameters | Biso mean: 83.6 Å2
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Refine analyze | Luzzati coordinate error obs: 0.47 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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LS refinement shell | Resolution: 2.9→3 Å
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