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Yorodumi- PDB-3se0: Structural characterization of the subunit A mutant F508W of the ... -
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-Basic information
Entry | Database: PDB / ID: 3se0 | ||||||
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Title | Structural characterization of the subunit A mutant F508W of the A-ATP synthase from Pyrococcus horikoshii | ||||||
Components | V-type ATP synthase alpha chain | ||||||
Keywords | HYDROLASE / A-Type ATP synthase / Adenine-binding pocket / Phenylalanine mutant | ||||||
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: 2.62 Å | ||||||
Authors | Tadwal, V.S. / Manimekalai, M.S.S. / Balakrishna, A.M. / Gruber, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Engineered tryptophan in the adenine-binding pocket of catalytic subunit A of A-ATP synthase demonstrates the importance of aromatic residues in adenine binding, forming a tool for steady- ...Title: Engineered tryptophan in the adenine-binding pocket of catalytic subunit A of A-ATP synthase demonstrates the importance of aromatic residues in adenine binding, forming a tool for steady-state and time-resolved fluorescence spectroscopy. Authors: Tadwal, V.S. / 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. / 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 | 3se0.cif.gz | 192.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3se0.ent.gz | 149.2 KB | Display | PDB format |
PDBx/mmJSON format | 3se0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3se0_validation.pdf.gz | 474.6 KB | Display | wwPDB validaton report |
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Full document | 3se0_full_validation.pdf.gz | 487.1 KB | Display | |
Data in XML | 3se0_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 3se0_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/3se0 ftp://data.pdbj.org/pub/pdb/validation_reports/se/3se0 | HTTPS FTP |
-Related structure data
Related structure data | 3sdzC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65714.703 Da / Num. of mol.: 1 / Fragment: UNP residues 1-240, 617-964 / Mutation: F508W Source method: isolated from a genetically manipulated source Details: The fusion protein of residues 1-240 and 617-964 of V-ATPase subunit A 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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-Non-polymers , 5 types, 150 molecules
#2: Chemical | ChemComp-SO4 / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: 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: 3.26 Å3/Da / Density % sol: 62.32 % |
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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: 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 | Resolution: 2.62→29.86 Å / Num. obs: 25400 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 11.8 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 44.1 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 6.57 / Num. unique all: 2425 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VDZ Resolution: 2.62→29.86 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.896 / SU B: 19.66 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R Free: 0.432 / 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: 65.151 Å2
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Refinement step | Cycle: LAST / Resolution: 2.62→29.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.617→2.685 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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