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- PDB-7szt: Crystal structure of Gdx-Clo from Small Multidrug Resistance fami... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7szt | ||||||
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Title | Crystal structure of Gdx-Clo from Small Multidrug Resistance family of transporters in low pH (protonated state) | ||||||
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![]() | TRANSPORT PROTEIN / Small Multidrug Resistance transporters / Membrane protein | ||||||
Function / homology | Small drug/metabolite transporter protein family / Small multidrug resistance protein / Small Multidrug Resistance protein / transmembrane transporter activity / plasma membrane / Dodecyldimethylphosphine oxide / Multidrug resistance protein, SMR family![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kermani, A.A. / Stockbridge, R.B. / Burata, O.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates. Authors: Kermani, A.A. / Burata, O.E. / Koff, B.B. / Koide, A. / Koide, S. / Stockbridge, R.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.9 KB | Display | ![]() |
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PDB format | ![]() | 124 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501.3 KB | Display | ![]() |
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Full document | ![]() | 518.1 KB | Display | |
Data in XML | ![]() | 27.3 KB | Display | |
Data in CIF | ![]() | 38 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mgxC ![]() 7mh6C ![]() 7ssuC ![]() 7sv9C ![]() 7svxC ![]() 7t00C ![]() 6wk8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11341.865 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HMPREF1982_00479 / Production host: ![]() ![]() #2: Antibody | Mass: 9931.934 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 71.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 40% PEG600, sodium acetate, pH 5.0, 100 mM calciium acetate, Apo12 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→107.21 Å / Num. obs: 26109 / % possible obs: 80.3 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.104 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.32→2.67 Å / Rmerge(I) obs: 0.4 / Num. unique obs: 1305 / CC1/2: 0.874 / Rsym value: 0.46 / % possible all: 45.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6WK8 Resolution: 2.32→32.68 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 44.32 / 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: 117.11 Å2 / Biso mean: 37.196 Å2 / Biso min: 9.21 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.32→32.68 Å
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LS refinement shell | Resolution: 2.32→2.405 Å / Rfactor Rfree error: 0
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