+Open data
-Basic information
Entry | Database: PDB / ID: 6s5d | |||||||||
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Title | Square conformation of KtrA R16A mutant ring with bound ATP | |||||||||
Components | Ktr system potassium uptake protein A | |||||||||
Keywords | TRANSPORT PROTEIN / RCK domain / potassium homeostasis / cation channel / magnesium / square conformation octameric ring / atp | |||||||||
Function / homology | Function and homology information monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.393 Å | |||||||||
Authors | Teixeira-Duarte, C.M. / Fonseca, F. / Morais-Cabral, J.H. | |||||||||
Funding support | Portugal, 2items
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Citation | Journal: Elife / Year: 2019 Title: Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site. Authors: Teixeira-Duarte, C.M. / Fonseca, F. / Morais Cabral, J.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s5d.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s5d.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 6s5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/6s5d ftp://data.pdbj.org/pub/pdb/validation_reports/s5/6s5d | HTTPS FTP |
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-Related structure data
Related structure data | 6s2jC 6s5bC 6s5cC 6s5eC 6s5gC 6s5nC 6s5oC 6s7rC 4j90S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 24830.645 Da / Num. of mol.: 2 / Mutation: R16A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / References: UniProt: O32080 #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | 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: 3.11 Å3/Da / Density % sol: 60.51 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 7.5 Details: 100mM HEPES-NaOH pH 7.5, 2% PEG 6000, 1% 2-Methyl-2,4-pentanediol (MPD) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.39→45.6 Å / Num. obs: 8535 / % possible obs: 99.8 % / Redundancy: 8.9 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.017 / Rrim(I) all: 0.05 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 3.39→3.66 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.829 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1724 / CC1/2: 0.573 / Rpim(I) all: 0.655 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4j90 Resolution: 3.393→45.598 Å / SU ML: 0.82 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 41.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.393→45.598 Å
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Refine LS restraints |
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LS refinement shell |
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