+Open data
-Basic information
Entry | Database: PDB / ID: 4xd7 | ||||||
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Title | Structure of thermophilic F1-ATPase inhibited by epsilon subunit | ||||||
Components | (ATP synthase ...) x 4 | ||||||
Keywords | HYDROLASE / F1-ATPASE / ATP SYNTHASE / ROTARY MOTOR PROTEIN / ROTATIONAL CATALYSIS / BACILLUS PS3 / THERMOPHILIC | ||||||
Function / homology | Function and homology information proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus sp. PS3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.9 Å | ||||||
Authors | SHIRAKIHARA, Y. / SHIRATORI, A. / TANIKAWA, H. / NAKASAKO, M. / YOSHIDA, M. / SUZUKI, T. | ||||||
Citation | Journal: Febs J. / Year: 2015 Title: Structure of a thermophilic F1 -ATPase inhibited by an epsilon-subunit: deeper insight into the epsilon-inhibition mechanism. Authors: Shirakihara, Y. / Shiratori, A. / Tanikawa, H. / Nakasako, M. / Yoshida, M. / Suzuki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xd7.cif.gz | 587.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xd7.ent.gz | 471.8 KB | Display | PDB format |
PDBx/mmJSON format | 4xd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/4xd7 ftp://data.pdbj.org/pub/pdb/validation_reports/xd/4xd7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-ATP synthase ... , 4 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 55317.543 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: atpA / Production host: Escherichia coli (E. coli) References: UniProt: Q5KUJ1, UniProt: P09219*PLUS, H+-transporting two-sector ATPase #2: Protein | Mass: 53949.949 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: atpD / Production host: Escherichia coli (E. coli) References: UniProt: Q5KUJ3, UniProt: P07677*PLUS, H+-transporting two-sector ATPase #3: Protein | | Mass: 32297.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: atpG / Production host: Escherichia coli (E. coli) / References: UniProt: Q5KUJ2, UniProt: P09222*PLUS #4: Protein | | Mass: 14773.485 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: atpC / Production host: Escherichia coli (E. coli) / References: UniProt: Q5KUJ4, UniProt: P07678*PLUS |
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-Non-polymers , 2 types, 5 molecules
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-ADP / | |
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-Details
Sequence details | Author states that the sequence reported for this entry (Bacillus PS3 F1) matches better to that of ...Author states that the sequence reported for this entry (Bacillus PS3 F1) matches better to that of available UNP reference sequence for Geobacillus kaustophilus (strain HTA426) 235909, so Q5KUJ1, Q5KUJ2, Q5KUJ3 and Q5KUJ4 were selected as database reference sequence in this structure instead of UNP P09219 ,P07677,P09222 and P07678 which are outdated. The accession number at GenBank are LC076382 (Bacillus_PS3_alpha, Bacillus_PS3_gamma, Bacillus_PS3_beta) and LC076383 (Bacillus_PS3_ epsilon). |
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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: 2.79 Å3/Da / Density % sol: 55.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: [drop]10 % PEG 6,000, 0.20 M sodium chloride, 0.05 M Tris-sulphate buffer (pH 8.0), 2mM DTT, 5mM CyDTA, 10% (v/v) ethyleneglycol and 10 mg/ml protein/ [reservoir] 14-16 % PEG 6,000, 0.2 M ...Details: [drop]10 % PEG 6,000, 0.20 M sodium chloride, 0.05 M Tris-sulphate buffer (pH 8.0), 2mM DTT, 5mM CyDTA, 10% (v/v) ethyleneglycol and 10 mg/ml protein/ [reservoir] 14-16 % PEG 6,000, 0.2 M sodium chloride, 0.05 M Tris-sulphate buffer (pH 8.0), 5mM CyDTA and 10% (v/v) ethyleneglycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97879 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97879 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→69.2 Å / Num. obs: 38420 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 3.9→4.11 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.3 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Starting model: 1SKY,1E79,1FS0 Resolution: 3.9→19.989 Å / SU ML: 0.43 / σ(F): 1.9 / Phase error: 27.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 88.442 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.9→19.989 Å
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Refine LS restraints |
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LS refinement shell |
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