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Yorodumi- PDB-3i73: Structural characterization for the nucleotide binding ability of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i73 | ||||||
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Title | Structural characterization for the nucleotide binding ability of subunit A with ADP of the A1AO ATP synthase | ||||||
Components | A-TYPE ATP SYNTHASE CATALYTIC SUBUNIT A | ||||||
Keywords | HYDROLASE | ||||||
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 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Manimekalai, S.M.S. / Kumar, A. / Balakrishna, A.M. / Gruber, G. | ||||||
Citation | 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. #1: 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 | 3i73.cif.gz | 126 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i73.ent.gz | 95.1 KB | Display | PDB format |
PDBx/mmJSON format | 3i73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/3i73 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/3i73 | HTTPS FTP |
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-Related structure data
Related structure data | 3i4lC 3i72C 3ikjC 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: 65775.805 Da / Num. of mol.: 1 / Fragment: UNP residues 1-240, 617-964 / Mutation: G79R Source method: isolated from a genetically manipulated source 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, 301 molecules
#2: Chemical | ChemComp-ADP / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Chemical | ChemComp-ACY / | #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: 3.29 Å3/Da / Density % sol: 62.65 % / Mosaicity: 0.326 ° |
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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: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 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: 2.4→30 Å / Num. all: 65278 / Num. obs: 34741 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 56.3 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.509 / Net I/σ(I): 53.19 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 5.13 / Num. unique all: 3415 / Χ2: 1.013 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VDZ Resolution: 2.4→27.72 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.225 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.828 / SU B: 6.046 / SU ML: 0.145 / SU R Cruickshank DPI: 0.296 / SU Rfree: 0.231 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.296 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: 128.11 Å2 / Biso mean: 57.496 Å2 / Biso min: 22.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→27.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.404→2.466 Å / Total num. of bins used: 20
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