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- PDB-3mfy: Structural characterization of the subunit A mutant F236A of the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mfy | ||||||
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Title | Structural characterization of the subunit A mutant F236A of the A-ATP synthase from Pyrococcus horikoshii | ||||||
![]() | V-type ATP synthase alpha chain | ||||||
![]() | HYDROLASE / A-Type ATP synthase / P loop / Phenylalanine mutant | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Balakrishna, A.M. / Kumar, A. / Manimekali, M.S.S. / Jeyakanthan, J. / Gruber, G. | ||||||
![]() | ![]() 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. #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. / Gerhard, G. #2: 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 | ![]() | 193.5 KB | Display | ![]() |
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PDB format | ![]() | 150.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.2 KB | Display | ![]() |
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Full document | ![]() | 494.8 KB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 37.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3m4yC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 65699.711 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT A (UNP residues 1-240, 617-964) / Mutation: G79R, F236A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O57728, H+-transporting two-sector ATPase | ||||||
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#2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-TRS / | #4: Chemical | ChemComp-ACY / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 50%(v/v) MPD, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 6, 2008 / 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: 2.35→50 Å / Num. all: 37346 / Num. obs: 35285 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Biso Wilson estimate: 41 Å2 / Rsym value: 0.064 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 10.2 % / Num. unique all: 3658 / Rsym value: 0.436 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1VDZ Resolution: 2.35→19.75 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.882 / SU B: 13.264 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.267 / ESU R Free: 0.235 / 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: 54.362 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→19.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.348→2.408 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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