+Open data
-Basic information
Entry | Database: PDB / ID: 4l73 | ||||||
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Title | Ca2+-bound MthK RCK domain at 2.5 Angstrom | ||||||
Components | Calcium-gated potassium channel MthK | ||||||
Keywords | METAL TRANSPORT / Rossmann Fold / regulatory domain / calcium binding / membrane-associated | ||||||
Function / homology | Function and homology information monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Smith, F.J. / Rothberg, B.S. | ||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Structural basis of allosteric interactions among Ca(2+)-binding sites in a K(+) channel RCK domain. Authors: Smith, F.J. / Pau, V.P. / Cingolani, G. / Rothberg, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l73.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l73.ent.gz | 152.2 KB | Display | PDB format |
PDBx/mmJSON format | 4l73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/4l73 ftp://data.pdbj.org/pub/pdb/validation_reports/l7/4l73 | HTTPS FTP |
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-Related structure data
Related structure data | 4l74C 4l75C 4l76C 2aefS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 26887.594 Da / Num. of mol.: 2 / Fragment: RCK domain (UNP residues 107-336) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: mthK, MTH_1520 / Production host: Escherichia coli (E. coli) / References: UniProt: O27564 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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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: 1.98 Å3/Da / Density % sol: 37.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 12% PEG4000, 1 M ammonium formate, 0.1 M sodium acetate, pH 4.8, 1 M calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→39.506 Å / Num. all: 14924 / Num. obs: 14924 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rsym value: 0.121 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.403 / % possible all: 89.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AEF Resolution: 2.5→39.506 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 24.01 / 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: 165.32 Å2 / Biso mean: 54.3949 Å2 / Biso min: 26.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→39.506 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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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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