+Open data
-Basic information
Entry | Database: PDB / ID: 6mwa | ||||||
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Title | NavAb Voltage-gated Sodium Channel, residues 1-239 | ||||||
Components | Ion transport protein | ||||||
Keywords | membrane protein / metal transport / Ion Channel Voltage-gated Sodium Channel | ||||||
Function / homology | Function and homology information voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Arcobacter butzleri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Lenaeus, M.J. / Catterall, W.A. | ||||||
Citation | Journal: J. Gen. Physiol. / Year: 2019 Title: Molecular dissection of multiphase inactivation of the bacterial sodium channel NaVAb. Authors: Gamal El-Din, T.M. / Lenaeus, M.J. / Ramanadane, K. / 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 | 6mwa.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mwa.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 6mwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mwa_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6mwa_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6mwa_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 6mwa_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/6mwa ftp://data.pdbj.org/pub/pdb/validation_reports/mw/6mwa | HTTPS FTP |
-Related structure data
Related structure data | 6mwbC 6mwdC 6mwgC 3rvyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29789.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria) Strain: RM4018 / Gene: Abu_1752 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5 | ||||||
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#2: Chemical | ChemComp-PX4 / #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.2 Å3/Da / Density % sol: 80.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 1.8 M Ammonium Sulfate 100mM Sodium Acetate pH 5.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 28623 / % possible obs: 97.4 % / Redundancy: 12.7 % / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.4→2.49 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RVY Resolution: 2.4→29.884 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.87 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.884 Å
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Refine LS restraints |
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LS refinement shell |
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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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