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Yorodumi- PDB-6wk5: Crystal structure of Gdx-Clo from Small Multidrug Resistance fami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wk5 | ||||||
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Title | Crystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters | ||||||
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 / 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: 3.5 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 | 6wk5.cif.gz | 82.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wk5.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 6wk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/6wk5 ftp://data.pdbj.org/pub/pdb/validation_reports/wk/6wk5 | HTTPS FTP |
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-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: 11529.445 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) 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: 4.34 Å3/Da / Density % sol: 71.69 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.1 M LiNO3, 0.1 M N-(2-Acetamido)iminodiacetic acid (ADA) pH 6.8, and 35% PEG 600 |
-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: 0.9786 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→54.14 Å / Num. obs: 10080 / % possible obs: 99.97 % / Redundancy: 7.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.035 / Rrim(I) all: 0.07 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 3.5→3.83 Å / Rmerge(I) obs: 0.148 / Num. unique obs: 2389 / CC1/2: 0.995 / Rpim(I) all: 0.086 / Rrim(I) all: 0.171 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.5→44.23 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 33.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 243.2 Å2 / Biso mean: 101.9386 Å2 / Biso min: 62.72 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→44.23 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %
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