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Open data
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Basic information
Entry | Database: PDB / ID: 4a01 | ||||||
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Title | Crystal Structure of the H-Translocating Pyrophosphatase | ||||||
![]() | PROTON PYROPHOSPHATASE | ||||||
![]() | HYDROLASE / MEMBRANE PROTEIN / PROTON PUMPING | ||||||
Function / homology | ![]() H+-exporting diphosphatase / diphosphate hydrolysis-driven proton transmembrane transporter activity / inorganic diphosphate phosphatase activity / vacuolar membrane / membrane => GO:0016020 / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, S.-M. / Tsai, J.-Y. / Hsiao, C.-D. / Chiu, C.-L. / Pan, R.-L. / Sun, Y.-J. | ||||||
![]() | ![]() Title: Crystal Structure of a Membrane Embedded H1-Translocating Pyrophosphatase Authors: Lin, S.-M. / Tsai, J.-Y. / Hsiao, C.-D. / Chiu, C.-L. / Pan, R.-L. / Sun, Y.-J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 292.9 KB | Display | ![]() |
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PDB format | ![]() | 245.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 62.7 KB | Display | |
Data in CIF | ![]() | 89 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 11 molecules AB![](data/chem/img/DMU.gif)
![](data/chem/img/DMU.gif)
#1: Protein | Mass: 80092.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O22124, UniProt: P21616*PLUS, inorganic diphosphatase #5: Sugar | ChemComp-DMU / |
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-Non-polymers , 4 types, 606 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/2PN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/2PN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE PROTEIN SEQUENCE OF ENTRY 4A01 HAD BEEN PUBLISHED AT PLANT PHYSIOL (1995) V.109, P1125-1127 AND ...THE PROTEIN SEQUENCE OF ENTRY 4A01 HAD BEEN PUBLISHED AT PLANT PHYSIOL (1995) V.109, P1125-1127 AND THE SEQUENCE OF RESIDUE 476 IS PHE. MEANWHILE, FROM THE ELECTRON DENSITY OMIT MAP, WE DETERMINED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→30 Å / Num. obs: 100220 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.84 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.074 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.995 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→30 Å
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Refine LS restraints |
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