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- PDB-3i72: Structural characterization for the nucleotide binding ability of... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3i72 | ||||||
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Title | Structural characterization for the nucleotide binding ability of subunit A with SO4 of the A1AO ATP synthase | ||||||
![]() | A-TYPE ATP SYNTHASE CATALYTIC SUBUNIT A | ||||||
![]() | HYDROLASE / ATP synthesis / ATP-binding / Autocatalytic cleavage / Hydrogen ion transport / Intron homing / Ion transport / Nuclease / Nucleotide-binding / Transport | ||||||
Function / homology | ![]() intein-mediated protein splicing / intron homing / 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, S.M.S. / Kumar, A. / Balakrishna, A.M. / Gruber, G. | ||||||
![]() | ![]() 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. #1: 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 | ![]() | 124.7 KB | Display | ![]() |
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PDB format | ![]() | 95.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.5 KB | Display | ![]() |
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Full document | ![]() | 496.4 KB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 36 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3i4lC ![]() 3i73C ![]() 3ikjC ![]() 1vdzS C: citing same article ( S: Starting model for refinement |
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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: UNP residues 1-240, 617-964 / Mutation: G79R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O57728, H+-transporting two-sector ATPase |
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-Non-polymers , 5 types, 315 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / | ||
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#3: Chemical | ChemComp-TRS / | ||
#4: Chemical | ChemComp-ACY / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.41 % / Mosaicity: 0.351 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 50% (v/v) MPD, 0.1 M 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 315 / Detector: CCD / Date: Apr 9, 2009 / 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: 2.47→30 Å / Num. all: 59295 / Num. obs: 31621 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 54.24 Å2 / Rmerge(I) obs: 0.057 / Χ2: 0.88 / Net I/σ(I): 28.68 |
Reflection shell | Resolution: 2.47→2.56 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.98 / Num. unique all: 3095 / Χ2: 0.843 / % possible all: 99.7 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1VDZ Resolution: 2.47→24.91 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.83 / SU B: 6.714 / SU ML: 0.156 / SU R Cruickshank DPI: 0.327 / SU Rfree: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.327 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: 116.26 Å2 / Biso mean: 55.321 Å2 / Biso min: 21.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.47→24.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.474→2.537 Å / Total num. of bins used: 20
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