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Yorodumi- PDB-8b5e: Exploring the ligand binding and conformational dynamics of recep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b5e | ||||||
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Title | Exploring the ligand binding and conformational dynamics of receptor domain 1 of the ABC transporter GlnPQ | ||||||
Components | ABC transporter permease subunit | ||||||
Keywords | TRANSPORT PROTEIN / Transporter / membrane protein | ||||||
Function / homology | Function and homology information peptide transport / ligand-gated monoatomic ion channel activity / ATP-binding cassette (ABC) transporter complex / protein transport Similarity search - Function | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Whittaker, J. / Guskov, A. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Exploring the ligand binding and conformational dynamics of receptor domain 1 of the ABC transporter GlnPQ Authors: Whittaker, J. / Guskov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b5e.cif.gz | 370 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b5e.ent.gz | 304.2 KB | Display | PDB format |
PDBx/mmJSON format | 8b5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/8b5e ftp://data.pdbj.org/pub/pdb/validation_reports/b5/8b5e | HTTPS FTP |
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-Related structure data
Related structure data | 8b5dC 6h30S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 24519.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Gene: glnP, AMHIJAGA_02474, GII02_01815 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: A0A2X0R690 |
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-Non-polymers , 6 types, 271 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
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-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: 2.02 Å3/Da / Density % sol: 39.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM NaCl 50 mM TRIS 10 % MPD 15 % PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2020 |
Radiation | Monochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→53.98 Å / Num. obs: 50688 / % possible obs: 99 % / Redundancy: 6 % / CC1/2: 0.96 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.6→3.5 Å / Num. unique obs: 49269 / CC1/2: 0.94 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H30 Resolution: 1.6→38.66 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 112.37 Å2 / Biso mean: 27.05 Å2 / Biso min: 12.75 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→38.66 Å
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