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Yorodumi- PDB-3nd8: Structural characterization for the nucleotide binding ability of... -
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-Basic information
Entry | Database: PDB / ID: 3nd8 | ||||||
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Title | Structural characterization for the nucleotide binding ability of subunit A of the A1AO ATP synthase | ||||||
Components | V-type ATP synthase alpha chain | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information intein-mediated protein splicing / intron homing / plant-type vacuole / proton motive force-driven plasma membrane ATP synthesis / fungal-type vacuole membrane / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / endonuclease activity ...intein-mediated protein splicing / intron homing / plant-type vacuole / proton motive force-driven plasma membrane ATP synthesis / fungal-type vacuole membrane / 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 | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kumar, A. / Gruber, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 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: Journal: J.Mol.Biol. / Year: 2010 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, S.M.S. / Balakrishna, A.M. / Jeyakanthan, J. / Gruber, 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nd8.cif.gz | 222.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nd8.ent.gz | 179.1 KB | Display | PDB format |
PDBx/mmJSON format | 3nd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/3nd8 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/3nd8 | HTTPS FTP |
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-Related structure data
Related structure data | 3nd9C 3p20C 1vdzS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: 65717.703 Da / Num. of mol.: 1 / Fragment: catalytic (UNP residues 1-240, 617-964) / Mutation: K240A, 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.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET22b(+)-His6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL References: UniProt: O57728, H+-transporting two-sector ATPase |
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-Non-polymers , 5 types, 286 molecules
#2: Chemical | ChemComp-MRD / ( #3: Chemical | #4: Chemical | ChemComp-ACY / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.97 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 7, 2009 |
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: 2.4→30 Å / Num. all: 34274 / Num. obs: 34060 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VDZ Resolution: 2.4→22.08 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.666 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(I): 3 / ESU R Free: 0.233 / 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: 56.611 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→22.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.402→2.464 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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