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Yorodumi- PDB-3m4y: Structural characterization of the subunit A mutant P235A of the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m4y | ||||||
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Title | Structural characterization of the subunit A mutant P235A of the A-ATP synthase | ||||||
Components | V-type ATP synthase alpha chain | ||||||
Keywords | HYDROLASE / ATP synthesis / ATP-binding / Autocatalytic cleavage / Hydrogen ion transport / Intron homing / Ion transport / Nuclease / Nucleotide-binding / Transport | ||||||
Function / homology | Function and homology information intron homing / intein-mediated protein splicing / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / endonuclease activity / Hydrolases; Acting on ester bonds / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii OT3 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Manimekalai, M.S. / Balakrishna, A.M. / Kumar, A. / Priya, R. / Biukovic, G. / Jeyakanthan, J. / Gruber, G. | ||||||
Citation | 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. / Balakrishna, A.M. / Priya, R. / Biukovic, G. / 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 | 3m4y.cif.gz | 246.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m4y.ent.gz | 198 KB | Display | PDB format |
PDBx/mmJSON format | 3m4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/3m4y ftp://data.pdbj.org/pub/pdb/validation_reports/m4/3m4y | HTTPS FTP |
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-Related structure data
Related structure data | 3mfyC 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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-Components
#1: Protein | Mass: 65649.625 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT A (UNP residues 1-240, 617-964) / Mutation: P235A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / 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 | ChemComp-MPD / ( #3: Chemical | ChemComp-TRS / | #4: Chemical | #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: 3.27 Å3/Da / Density % sol: 62.34 % / Mosaicity: 0.46 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 35% (v/v) MPD, 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: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 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 | Redundancy: 7.9 % / Av σ(I) over netI: 46 / Number: 280801 / Rmerge(I) obs: 0.04 / Χ2: 0.89 / D res high: 2.38 Å / D res low: 30 Å / Num. obs: 35394 / % possible obs: 99.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.38→30 Å / Num. all: 35507 / Num. obs: 35394 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 50.3 Å2 / Rmerge(I) obs: 0.04 / Χ2: 0.886 / Net I/σ(I): 17.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.38→2.47 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 5.76 / Num. unique all: 3482 / Χ2: 0.841 / % possible all: 99.9 |
-Phasing
Phasing MR | Rfactor: 33.37 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1VDZ Resolution: 2.38→24.93 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 12.69 / SU ML: 0.142 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.286 / ESU R Free: 0.239 / 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: 101.35 Å2 / Biso mean: 56.594 Å2 / Biso min: 12.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→24.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.441 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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