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Yorodumi- PDB-5aw9: Kinetics by X-ray crystallography: native E2.MgF42-.2K+ crystal f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aw9 | |||||||||||||||
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Title | Kinetics by X-ray crystallography: native E2.MgF42-.2K+ crystal for Rb+ bound crystals | |||||||||||||||
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: 2.8 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 | 5aw9.cif.gz | 276.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aw9.ent.gz | 215.4 KB | Display | PDB format |
PDBx/mmJSON format | 5aw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/5aw9 ftp://data.pdbj.org/pub/pdb/validation_reports/aw/5aw9 | 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 5aw3C 5aw4C 5aw5C 5aw6C 5aw7C 5aw8C 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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#9: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 135 molecules
#5: Chemical | ChemComp-MF4 / | ||||
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#6: Chemical | ChemComp-MG / | ||||
#7: Chemical | #8: Chemical | ChemComp-CLR / | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.18 % |
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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: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 23, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 40891 / % possible obs: 93.6 % / Redundancy: 3.5 % / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.8→2.89 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZXE Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 18.213 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 92.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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