[English] 日本語
Yorodumi- PDB-8oyf: Crystal structure of ASBTNM in lipidic cubic phase without substr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oyf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ASBTNM in lipidic cubic phase without substrate bound | ||||||
Components | TransporterTransport protein | ||||||
Keywords | TRANSPORT PROTEIN / Secondary Membrane Transporter | ||||||
Function / homology | Bile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily / membrane / NICKEL (II) ION / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATIDYLETHANOLAMINE / Transporter Function and homology information | ||||||
Biological species | Neisseria meningitidis MC58 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Becker, P. / Cameron, A.D. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Biorxiv / Year: 2023 Title: Mechanism of substrate binding and transport in BASS transporters. Authors: Becker, P. / Naughton, F.B. / Brotherton, D.H. / Pacheco-Gomez, R. / Beckstein, O. / Cameron, A.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8oyf.cif.gz | 227.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8oyf.ent.gz | 150.6 KB | Display | PDB format |
PDBx/mmJSON format | 8oyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/8oyf ftp://data.pdbj.org/pub/pdb/validation_reports/oy/8oyf | HTTPS FTP |
---|
-Related structure data
Related structure data | 8oygC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33836.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Gene: NMB0705 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K0A9 |
---|
-Non-polymers , 6 types, 43 molecules
#2: Chemical | #3: Chemical | ChemComp-PTY / | #4: Chemical | #5: Chemical | ChemComp-NI / | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.72 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7 Details: 0.1M Sodium Chloride, 0.1M Hepes pH 7.0, 30% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→59 Å / Num. obs: 20744 / % possible obs: 99.37 % / Redundancy: 7.1 % / Biso Wilson estimate: 30.01 Å2 / CC1/2: 0.957 / CC star: 0.989 / Rmerge(I) obs: 0.1356 / Rpim(I) all: 0.05402 / Rrim(I) all: 0.1467 / Net I/σ(I): 6.68 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.8541 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 14741 / CC1/2: 0.658 / CC star: 0.891 / Rpim(I) all: 0.3315 / Rrim(I) all: 0.9198 / % possible all: 99.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→58.96 Å / SU ML: 0.2151 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3578 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→58.96 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 3.36249657173 Å / Origin y: -9.71381233022 Å / Origin z: -19.890386443 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |