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Yorodumi- PDB-6wk8: Crystal structure of Gdx-Clo from Small Multidrug Resistance fami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wk8 | ||||||
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Title | Crystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters in complex with phenylguanidinium | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Small Multidrug Resistance / guanidinium transporter / EmrE homologue / dual topology protein | ||||||
Function / homology | Small drug/metabolite transporter protein family / Small multidrug resistance protein / Small Multidrug Resistance protein / transmembrane transporter activity / plasma membrane / Dodecyldimethylphosphine oxide / 1-phenylguanidine / Multidrug resistance protein, SMR family Function and homology information | ||||||
Biological species | Clostridiales bacterium oral taxon 876 str. F0540 (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.53 Å | ||||||
Authors | Kermani, A.A. / Stockbridge, R.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: The structural basis of promiscuity in small multidrug resistance transporters. Authors: Kermani, A.A. / Macdonald, C.B. / Burata, O.E. / Ben Koff, B. / Koide, A. / Denbaum, E. / Koide, S. / Stockbridge, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wk8.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wk8.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 6wk8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wk8_validation.pdf.gz | 930.2 KB | Display | wwPDB validaton report |
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Full document | 6wk8_full_validation.pdf.gz | 940.5 KB | Display | |
Data in XML | 6wk8_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6wk8_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/6wk8 ftp://data.pdbj.org/pub/pdb/validation_reports/wk/6wk8 | HTTPS FTP |
-Related 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: 11341.865 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridiales bacterium oral taxon 876 str. F0540 (bacteria) Gene: HMPREF1982_00479 / Plasmid: pET-21c / Production host: Escherichia coli (E. coli) / References: UniProt: U2EQ00 #2: Antibody | Mass: 9931.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-PL0 / | #4: Chemical | ChemComp-9PD / | #5: Sugar | ChemComp-DMU / | 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: 4.3 Å3/Da / Density % sol: 71.42 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 100 mM LiNaSO4, 0.1 M Tris pH 8.75, 34% PEG 600 / PH range: 8.75 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→59 Å / Num. obs: 9466 / % possible obs: 85 % / Redundancy: 7.1 % / CC1/2: 0.946 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.057 / Rrim(I) all: 0.145 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.5→3 Å / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 473 / CC1/2: 0.807 / Rpim(I) all: 0.438 / Rrim(I) all: 0.723 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.53→58.39 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.77 / SU B: 11.895 / SU ML: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.644 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.24 Å2 / Biso mean: 52.447 Å2 / Biso min: 27.42 Å2
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Refinement step | Cycle: final / Resolution: 2.53→58.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.533→2.598 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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