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Yorodumi- PDB-2i4r: Crystal structure of the V-type ATP synthase subunit F from Archa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i4r | ||||||
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Title | Crystal structure of the V-type ATP synthase subunit F from Archaeoglobus fulgidus. NESG target GR52A. | ||||||
Components | V-type ATP synthase subunit F | ||||||
Keywords | HYDROLASE / NESG / GR52A / ATP synthesis / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase activity, rotational mechanism / ATP binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Vorobiev, S.M. / Su, M. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the V-type ATP synthase subunit F from Archaeoglobus fulgidus Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i4r.cif.gz | 39.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i4r.ent.gz | 30.3 KB | Display | PDB format |
PDBx/mmJSON format | 2i4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/2i4r ftp://data.pdbj.org/pub/pdb/validation_reports/i4/2i4r | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11664.771 Da / Num. of mol.: 2 / Mutation: I51M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: atpF / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic References: UniProt: O29102, H+-transporting two-sector ATPase #2: Water | ChemComp-HOH / | |
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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: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 15-20% PEG 1000, 150 mM KH(2)PO(4), 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97900, 0.97918, 0.96774 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 13, 2006 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→30 Å / Num. all: 10771 / Num. obs: 10674 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.062 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.06 / Num. unique all: 1068 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→29.14 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 205705.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.8787 Å2 / ksol: 0.257732 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.071 / Total num. of bins used: 6
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Xplor file |
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