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Yorodumi- PDB-3rvy: Crystal structure of the NavAb voltage-gated sodium channel (Ile2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rvy | ||||||
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Title | Crystal structure of the NavAb voltage-gated sodium channel (Ile217Cys, 2.7 A) | ||||||
Components | Ion transport proteinIon transporter | ||||||
Keywords | METAL TRANSPORT / tetrameric ion channel / voltage-gated sodium-selective ion channel / membrane | ||||||
Function / homology | Function and homology information monoatomic cation channel activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Arcobacter butzleri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Payandeh, J. / Scheuer, T. / Zheng, N. / Catterall, W.A. | ||||||
Citation | Journal: Nature / Year: 2011 Title: The crystal structure of a voltage-gated sodium channel. Authors: Payandeh, J. / Scheuer, T. / Zheng, N. / Catterall, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rvy.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rvy.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 3rvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/3rvy ftp://data.pdbj.org/pub/pdb/validation_reports/rv/3rvy | 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: 33105.094 Da / Num. of mol.: 2 / Mutation: I217C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arcobacter butzleri (bacteria) / Strain: RM4018 / Gene: Abu_1752 / Plasmid: pFastBac Dual / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A8EVM5 #2: Chemical | ChemComp-PX4 / #3: Water | ChemComp-HOH / | |
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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: 5.72 Å3/Da / Density % sol: 78.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.75 Details: CHAPSO:DMPC bicelles, 2 M ammonium sulphate, 0.1 M Na-citrate pH 4.75, 28% glucose, 0.01 M YCl3, nicotinic acid (sat.), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99994 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2010 |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99994 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 42048 / Num. obs: 36497 / % possible obs: 86.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 23.12 |
Reflection shell | Resolution: 2.7→2.76 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 1.69 / % possible all: 55.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber Details: Built using SAD data sets from Hg and SeMet crystals
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.73 Å
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