+Open data
-Basic information
Entry | Database: PDB / ID: 7mdj | ||||||
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Title | The structure of KcsA in complex with a synthetic Fab | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / ion channel | ||||||
Function / homology | Potassium channel domain / Ion channel / monoatomic ion transmembrane transport / identical protein binding / plasma membrane / : / pH-gated potassium channel KcsA Function and homology information | ||||||
Biological species | synthetic construct (others) Streptomyces lividans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Rohaim, A. / Slezak, T. / Blackowicz, L. / Kossiakoff, A. / Roux, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Gen.Physiol. / Year: 2022 Title: Engineering of a synthetic antibody fragment for structural and functional studies of K+ channels. Authors: Rohaim, A. / Slezak, T. / Koh, Y.H. / Blachowicz, L. / Kossiakoff, A.A. / Roux, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mdj.cif.gz | 216.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mdj.ent.gz | 173.3 KB | Display | PDB format |
PDBx/mmJSON format | 7mdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/7mdj ftp://data.pdbj.org/pub/pdb/validation_reports/md/7mdj | HTTPS FTP |
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-Related structure data
Related structure data | 6w0iS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 24379.131 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) | ||||
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#2: Antibody | Mass: 23604.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) | ||||
#3: Protein | Mass: 13211.582 Da / Num. of mol.: 1 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 | ||||
#4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 50 mM sodium acetate/50 mM ammonium acetate, 50 mM magnesium acetate, 25% PEG 400. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50.01 Å / Num. obs: 17621 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.99 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.7→2.75 Å / Num. unique obs: 17621 / CC1/2: 0.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6W0I Resolution: 2.75→50.01 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.953 / SU B: 45.775 / SU ML: 0.414 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.423 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 401.98 Å2 / Biso mean: 122.052 Å2 / Biso min: 67.19 Å2
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Refinement step | Cycle: final / Resolution: 2.75→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.751→2.822 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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