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Yorodumi- PDB-5aw3: Kinetics by X-ray crystallography: Tl+-substitution of bound K+ i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aw3 | |||||||||||||||
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Title | Kinetics by X-ray crystallography: Tl+-substitution of bound K+ in the E2.MgF42-.2K+ crystal after 100 min | |||||||||||||||
Components |
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Keywords | HYDROLASE/TRANSPORT PROTEIN / MEMBRANE PROTEIN / ION PUMP / ATPASE / K+ BINDING / HALOACID DEHYDROGENEASE SUPERFAMILY / PHOSPHATE ANALOGUE / ATP-BINDING / HYDROLASE / ION TRANSPORT / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / HYDROLASE-TRANSPORT PROTEIN COMPLEX / KINETICS | |||||||||||||||
Function / homology | Function and homology information regulation of monoatomic ion transport / P-type potassium transmembrane transporter activity / sodium:potassium-exchanging ATPase complex / ion channel regulator activity / sodium ion transport / monoatomic ion transport / potassium ion transport / ATP hydrolysis activity / ATP binding / membrane ...regulation of monoatomic ion transport / P-type potassium transmembrane transporter activity / sodium:potassium-exchanging ATPase complex / ion channel regulator activity / sodium ion transport / monoatomic ion transport / potassium ion transport / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Squalus acanthias (spiny dogfish) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å | |||||||||||||||
Authors | Ogawa, H. / Cornelius, F. / Hirata, A. / Toyoshima, C. | |||||||||||||||
Funding support | Japan, Denmark, 4items
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Citation | Journal: Nat Commun / Year: 2015 Title: Sequential substitution of K(+) bound to Na(+),K(+)-ATPase visualized by X-ray crystallography. Authors: Ogawa, H. / Cornelius, F. / Hirata, A. / Toyoshima, C. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aw3.cif.gz | 269.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aw3.ent.gz | 209.3 KB | Display | PDB format |
PDBx/mmJSON format | 5aw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/5aw3 ftp://data.pdbj.org/pub/pdb/validation_reports/aw/5aw3 | HTTPS FTP |
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-Related structure data
Related structure data | 5avqC 5avrC 5avsC 5avtC 5avuC 5avvC 5avwC 5avxC 5avyC 5avzC 5aw0C 5aw1C 5aw2C 5aw4C 5aw5C 5aw6C 5aw7C 5aw8C 5aw9C 2zxeS 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
-Protein , 3 types, 3 molecules ABG
#1: Protein | Mass: 113309.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Squalus acanthias (spiny dogfish) / References: UniProt: Q4H132 |
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#2: Protein | Mass: 35176.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Squalus acanthias (spiny dogfish) / References: UniProt: C4IX13 |
#3: Protein | Mass: 8225.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Squalus acanthias (spiny dogfish) / References: UniProt: Q70Q12 |
-Sugars , 2 types, 2 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#10: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 8 molecules
#5: Chemical | ChemComp-MF4 / | ||||||
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#6: Chemical | ChemComp-MG / | ||||||
#7: Chemical | #8: Chemical | ChemComp-K / | #9: Chemical | ChemComp-CLR / | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.16 % |
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 7 Details: PEG 3000, MPD, potassium acetate, potassium chloride, magnesium chloride, potassium fluoride, MES/TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9785 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→50 Å / Num. obs: 26118 / % possible obs: 99.3 % / Redundancy: 3.6 % / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 3.35→3.44 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZXE Resolution: 3.35→14.97 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 5451843.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3.5 / Details: BULK SOLVENT MODEL USED, Rigid body refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.21 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 140.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.35→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.35→3.56 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
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Xplor file |
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