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Yorodumi- PDB-7rp0: Structural Snapshots of Intermediates in the Gating of a K+ Channel -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rp0 | ||||||
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Title | Structural Snapshots of Intermediates in the Gating of a K+ Channel | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Ion channel / KcsA | ||||||
Function / homology | Function and homology information delayed rectifier potassium channel activity / voltage-gated potassium channel complex / identical protein binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Streptomyces lividans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | ||||||
Authors | Reddi, R. / Matulef, K. / Riederer, E.A. / Valiyaveetil, F.I. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2021 Title: Structures of Gating Intermediates in a K + channell. Authors: Reddi, R. / Matulef, K. / Riederer, E. / Moenne-Loccoz, P. / Valiyaveetil, F.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rp0.cif.gz | 120.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rp0.ent.gz | 89.5 KB | Display | PDB format |
PDBx/mmJSON format | 7rp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rp0_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 7rp0_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 7rp0_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 7rp0_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/7rp0 ftp://data.pdbj.org/pub/pdb/validation_reports/rp/7rp0 | HTTPS FTP |
-Related structure data
Related structure data | 7m2hC 7m2iC 7m2jC 1k4cS 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
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 10896.655 Da / Num. of mol.: 1 / Fragment: UNP residues 22-124 / Mutation: Y82A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334 |
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-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 23411.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23435.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
-Non-polymers , 5 types, 44 molecules
#4: Chemical | ChemComp-F09 / | ||||||
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#5: Chemical | ChemComp-K / #6: Chemical | ChemComp-TBA / | #7: Chemical | ChemComp-DGA / | #8: Water | ChemComp-HOH / | |
-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: 3.98 Å3/Da / Density % sol: 69.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.25 Details: 50 mM MES, pH 6.25, 50 mM magnesium acetate, 27% PEG400 PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.000032 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000032 Å / Relative weight: 1 |
Reflection | Resolution: 2.478→54.98 Å / Num. obs: 58647 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.99 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.48→2.58 Å / Num. unique obs: 3643 / CC1/2: 0.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1K4C Resolution: 2.48→54.917 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.59 / 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: 106.83 Å2 / Biso mean: 55.3944 Å2 / Biso min: 19.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.48→54.917 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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