+Open data
-Basic information
Entry | Database: PDB / ID: 7pgh | ||||||||||||
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Title | NaVAe1/Sp1CTDp (DDM) | ||||||||||||
Components | Ion transport protein,Voltage-gated sodium channel subunit | ||||||||||||
Keywords | MEMBRANE PROTEIN / ion channel membrane protein transport protein antibody complex | ||||||||||||
Function / homology | Function and homology information voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity / sodium ion transport / membrane => GO:0016020 / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Alkalilimnicola ehrlichii (bacteria) Ruegeria pomeroyi (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4.194 Å | ||||||||||||
Authors | Lolicato, M. / Arrigoni, C. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2022 Title: Quaternary structure independent folding of voltage-gated ion channel pore domain subunits. Authors: Arrigoni, C. / Lolicato, M. / Shaya, D. / Rohaim, A. / Findeisen, F. / Fong, L.K. / Colleran, C.M. / Dominik, P. / Kim, S.S. / Schuermann, J.P. / DeGrado, W.F. / Grabe, M. / Kossiakoff, A.A. / Minor Jr., D.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pgh.cif.gz | 224.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pgh.ent.gz | 189.5 KB | Display | PDB format |
PDBx/mmJSON format | 7pgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pgh_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7pgh_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7pgh_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 7pgh_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/7pgh ftp://data.pdbj.org/pub/pdb/validation_reports/pg/7pgh | HTTPS FTP |
-Related structure data
Related structure data | 7pg8C 7pgbC 7pgfC 7pggC 7pgiC 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, 8 molecules FABCDEGH
#1: Protein | Mass: 16356.166 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkalilimnicola ehrlichii (strain ATCC BAA-1101 / DSM 17681 / MLHE-1) (bacteria), (gene. exp.) Ruegeria pomeroyi (bacteria) Strain: ATCC BAA-1101 / DSM 17681 / MLHE-1 / Gene: Mlg_0322 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0ABW0, UniProt: Q6TMY8 |
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-Non-polymers , 5 types, 19 molecules
#2: Chemical | ChemComp-PE4 / #3: Chemical | ChemComp-D12 / #4: Chemical | ChemComp-OCT / | #5: Chemical | #6: Chemical | |
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-Details
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: 4.94 Å3/Da / Density % sol: 75.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Purified NaVAe1Sp1CTDp was concentrated to 13-13.5 mg ml-1 and crystallized in 22% PEG3350, 0.3 M KI, 8 mM sarcosine. Crystals were harvested in 30% PEG3350, 0.3 M KI, 8 mM sarcosine and 1mM ...Details: Purified NaVAe1Sp1CTDp was concentrated to 13-13.5 mg ml-1 and crystallized in 22% PEG3350, 0.3 M KI, 8 mM sarcosine. Crystals were harvested in 30% PEG3350, 0.3 M KI, 8 mM sarcosine and 1mM Fos-choline 12 (FC-12), Anatrace). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1, 0.97698, 0.97953, 0.95368 | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2017 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 4.194→15 Å / Num. obs: 18983 / % possible obs: 96.53 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.6 | |||||||||||||||
Reflection shell | Resolution: 4.194→4.342 Å / Rmerge(I) obs: 1 / Num. unique obs: 1766 / CC1/2: 0.404 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 4.194→14.989 Å / SU ML: 1.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 50.69 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 650.8 Å2 / Biso mean: 317.5867 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.194→14.989 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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