+Open data
-Basic information
Entry | Database: PDB / ID: 6jxj | ||||||
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Title | Rb+-bound E2-AlF state of the gastric proton pump (Tyr799Trp) | ||||||
Components | (Potassium-transporting ATPase ...) x 2 | ||||||
Keywords | MEMBRANE PROTEIN / P-type ATPase / proton pump / gastric / ion pump | ||||||
Function / homology | Function and homology information H+/K+-exchanging ATPase / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane ...H+/K+-exchanging ATPase / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / potassium ion binding / ATPase activator activity / potassium ion transmembrane transport / proton transmembrane transport / cell adhesion / apical plasma membrane / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Abe, K. / Irie, K. | ||||||
Citation | Journal: Elife / Year: 2019 Title: A single K + -binding site in the crystal structure of the gastric proton pump. Authors: Yamamoto, K. / Dubey, V. / Irie, K. / Nakanishi, H. / Khandelia, H. / Fujiyoshi, Y. / Abe, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jxj.cif.gz | 569.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jxj.ent.gz | 442.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jxj_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6jxj_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6jxj_validation.xml.gz | 56.2 KB | Display | |
Data in CIF | 6jxj_validation.cif.gz | 77.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/6jxj ftp://data.pdbj.org/pub/pdb/validation_reports/jx/6jxj | HTTPS FTP |
-Related structure data
Related structure data | 6jxhC 6jxiC 6jxkC 5yluS S: Starting model for refinement C: citing same article (ref.) |
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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
-Potassium-transporting ATPase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 109220.711 Da / Num. of mol.: 1 / Mutation: R220C, S593C, Y799W, G1005S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: ATP4A / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / Variant (production host): GnT1- / References: UniProt: P19156, H+/K+-exchanging ATPase |
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#2: Protein | Mass: 32982.652 Da / Num. of mol.: 1 / Mutation: R220C, S593C, Y799W, G1005S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: ATP4B / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / Variant (production host): GnT1- / References: UniProt: P18434 |
-Sugars , 1 types, 6 molecules
#9: Sugar | ChemComp-NAG / |
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-Non-polymers , 7 types, 387 molecules
#3: Chemical | ChemComp-MG / | ||||||||||
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#4: Chemical | ChemComp-PCW / #5: Chemical | ChemComp-CE1 / | #6: Chemical | ChemComp-ALF / | #7: Chemical | ChemComp-RB / #8: Chemical | ChemComp-CLR / | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% glycerol, 20% PEG2000MME, 0.4 M RbCl, 3% methylpentanediol, 5 mM beta-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 61014 / % possible obs: 76 % / Redundancy: 8 % / Biso Wilson estimate: 48.43 Å2 / CC1/2: 0.99 / Net I/σ(I): 11.64 |
Reflection shell | Resolution: 2.5→2.6 Å / Mean I/σ(I) obs: 0.77 / Num. unique obs: 61013 / CC1/2: 0.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ylu Resolution: 2.5→49.71 Å / SU ML: 0.364 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.3055 / Stereochemistry target values: GeoStd + Monomer Library
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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 mean: 60.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→49.71 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 34.7785 Å / Origin y: -33.2659 Å / Origin z: -41.184 Å
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Refinement TLS group |
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