[English] 日本語
![](img/lk-miru.gif)
- PDB-3qia: Crystal structure of P-loop G237A mutant of subunit A of the A1AO... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3qia | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of P-loop G237A mutant of subunit A of the A1AO ATP synthase | ||||||
![]() | V-type ATP synthase alpha chain | ||||||
![]() | HYDROLASE / ATP Binding | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Ragunathan, P. / Manimekalai, M.S.S. / Jeyakanthan, J. / Gruber, G. | ||||||
![]() | ![]() Title: Conserved glycine residues in the P-loop of ATP synthases form a doorframe for nucleotide entrance. Authors: Priya, R. / Kumar, A. / Manimekalai, M.S. / 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.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.S. / Balakrishna, A.M. / Priya, R. / Biukovic, G. / Jeyakanthan, J. / Gruber, G. #3: Journal: Acta Crystallogr.,Sect.C / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 247.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 201.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 484.7 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qg1C ![]() 3qjyC ![]() 1vdzS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 65689.688 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT A (UNP residues 1-240, 617-964) / Mutation: G237A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O57728, H+-transporting two-sector ATPase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-ACY / #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.28 % / Mosaicity: 0.293 ° |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 50% (v/v) MPD, 2mM MgADP and 0.1 M acetate (pH 4.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 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: 2.6→30 Å / Num. all: 28040 / Num. obs: 27986 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 57.45 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.014 / Net I/σ(I): 12.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1VDZ Resolution: 2.6→27.32 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.881 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 23.547 / SU ML: 0.232 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.496 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 238.6 Å2 / Biso mean: 66.382 Å2 / Biso min: 10.01 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→27.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 23.2138 Å / Origin y: -35.4784 Å / Origin z: -6.0841 Å
|