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- PDB-3p20: Crystal structure of vanadate bound subunit A of the A1AO ATP synthase -
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Open data
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Basic information
Entry | Database: PDB / ID: 3p20 | ||||||
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Title | Crystal structure of vanadate bound subunit A of the A1AO ATP synthase | ||||||
![]() | V-type ATP synthase alpha chain | ||||||
![]() | HYDROLASE / ATP Binding | ||||||
Function / homology | ![]() intron homing / intein-mediated protein splicing / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / endonuclease activity / Hydrolases; Acting on ester bonds / lysosomal membrane / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Manimekalai, M.S.S. / Kumar, A. / Jeyakanthan, J. / Gruber, G. | ||||||
![]() | ![]() Title: The transition-like state and Pi entrance into the catalytic a subunit of the biological engine A-ATP synthase. Authors: Manimekalai, M.S. / Kumar, A. / Jeyakanthan, J. / Gruber, G. #1: ![]() Title: Nucleotide binding states of subunit A of the A-ATP synthase and the implication of P-loop switch in evolution. Authors: Kumar, A. / Manimekalai, M.S. / Balakrishna, A.M. / Jeyakanthan, J. / Gruber, G. #2: ![]() Title: The critical roles of residues P235 and F236 of subunit A of the motor protein A-ATP synthase in P-loop formation and nucleotide binding. Authors: Kumar, A. / Manimekalai, M.S. / Balakrishna, A.M. / Priya, R. / Biukovic, G. / Jeyakanthan, J. / Gruber, G. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Structure of the catalytic nucleotide-binding subunit A of A-type ATP synthase from Pyrococcus horikoshii reveals a novel domain related to the peripheral stalk. Authors: Maegawa, Y. / Morita, H. / Iyaguchi, D. / Yao, M. / Watanabe, N. / Tanaka, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.7 KB | Display | ![]() |
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PDB format | ![]() | 177.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.7 KB | Display | ![]() |
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Full document | ![]() | 503.8 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nd8C ![]() 3nd9C ![]() 1vdzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65775.805 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT (UNP residues 1-240, 617-964) / Mutation: G79R Source method: isolated from a genetically manipulated source Details: THE FUSION OF RESIDUES 1-240 AND RESIDUES 617-964 from V-ATPase subunit A Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O57728, H+-transporting two-sector ATPase |
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-Non-polymers , 5 types, 97 molecules ![](data/chem/img/VO4.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ACY / #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.77 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 50% (v/v) MPD, 2mM sodium orthovanadate, 2mM Magnesium chloride and 0.1M acetate (pH 4.5), vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 8, 2010 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→30 Å / Num. all: 20571 / Num. obs: 20534 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 69.93 Å2 / Rmerge(I) obs: 0.087 / Χ2: 0.593 / Net I/σ(I): 7.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 32.79 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1vdz Resolution: 2.85→29.25 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / SU B: 22.74 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.334 / 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 max: 168.33 Å2 / Biso mean: 50.3054 Å2 / Biso min: 4.09 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→29.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.855→2.928 Å / Total num. of bins used: 20
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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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