+Open data
-Basic information
Entry | Database: PDB / ID: 6v4b | ||||||
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Title | DeCLIC N-terminal Domain 34-202 | ||||||
Components | Neur_chan_LBD domain-containing protein | ||||||
Keywords | TRANSPORT PROTEIN / ion channel / N-terminal extension domain | ||||||
Function / homology | Function and homology information extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane Similarity search - Function | ||||||
Biological species | uncultured Desulfofustis sp. PB-SRB1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||
Authors | Delarue, M. / Hu, H.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel. Authors: Hu, H. / Howard, R.J. / Bastolla, U. / Lindahl, E. / Delarue, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v4b.cif.gz | 147.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v4b.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 6v4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/6v4b ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v4b | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22105.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured Desulfofustis sp. PB-SRB1 (bacteria) Gene: N839_03575 / Production host: Escherichia coli (E. coli) / References: UniProt: V4JF97 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.14 Å3/Da / Density % sol: 42.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 6.5, 0.7 M NaH2PO4, 0.7 M KH2PO4. |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40.75 Å / Num. obs: 37644 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 32.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.75→1.79 Å / Rmerge(I) obs: 1.21 / Num. unique obs: 2724 / CC1/2: 0.652 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.75→24.84 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.106
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Displacement parameters | Biso max: 149.07 Å2 / Biso mean: 37.98 Å2 / Biso min: 20.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→24.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.8 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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