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Yorodumi- PDB-3qjy: Crystal structure of P-loop G234A mutant of subunit A of the A1AO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qjy | ||||||
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Title | Crystal structure of P-loop G234A mutant of subunit A of the A1AO ATP synthase | ||||||
Components | V-type ATP synthase alpha chain | ||||||
Keywords | HYDROLASE / ATP Binding | ||||||
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 / molecular replacement / Resolution: 2.35 Å | ||||||
Authors | Ragunathan, P. / Manimekalai, M.S.S. / Jeyakanthan, J. / Gruber, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 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: 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, M.S.S. / Balakrishna, A.M. / Jeyakanthan, J. / Gruber, G. #2: Journal: J.Mol.Biol. / Year: 2010 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qjy.cif.gz | 245.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qjy.ent.gz | 199.3 KB | Display | PDB format |
PDBx/mmJSON format | 3qjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qjy_validation.pdf.gz | 468.8 KB | Display | wwPDB validaton report |
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Full document | 3qjy_full_validation.pdf.gz | 483.2 KB | Display | |
Data in XML | 3qjy_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 3qjy_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/3qjy ftp://data.pdbj.org/pub/pdb/validation_reports/qj/3qjy | HTTPS FTP |
-Related structure data
Related structure data | 3qg1C 3qiaC 1vdzS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 65689.688 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT A (UNP residues 1-240, 617-964) / Mutation: G234A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: atpA, PH1975 / 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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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 50% (v/v) MPD, 2mM MgADP, 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 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: 2.35→30 Å / Num. all: 37374 / Num. obs: 37307 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 47.29 Å2 / Rmerge(I) obs: 0.055 / Χ2: 0.439 / Net I/σ(I): 8.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VDZ Resolution: 2.35→29.83 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.642 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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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: 132.3 Å2 / Biso mean: 59.481 Å2 / Biso min: 14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.349→2.41 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -35.7108 Å / Origin y: -22.8195 Å / Origin z: 19.9843 Å
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