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Yorodumi- PDB-2qai: Crystal structure of the V-type ATP synthase subunit F from Pyroc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qai | ||||||
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Title | Crystal structure of the V-type ATP synthase subunit F from Pyrococcus furiosus. NESG target PfR7. | ||||||
Components | V-type ATP synthase subunit F | ||||||
Keywords | HYDROLASE / ATP SYNTHASE / SUBUNIT F / VATF_PYRFU / atpF / NESG / 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 | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Vorobiev, S.M. / Su, M. / Seetharaman, J. / Ma, L.-C. / Shih, L. / Fang, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Ma, L.-C. / Shih, L. / Fang, Y. / 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 Pyrococcus furiosus. Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Ma, L.-C. / Shih, L. / Fang, Y. / Xiao, R. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE LIGHT SCATTERING DATA ALSO SHOW THAT THE PROTEIN EXISTS AS A DIMER IN SOLUTION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qai.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qai.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qai_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 2qai_full_validation.pdf.gz | 439.1 KB | Display | |
Data in XML | 2qai_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 2qai_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/2qai ftp://data.pdbj.org/pub/pdb/validation_reports/qa/2qai | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12921.538 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: Vc1, DSM 3638, JCM 8422 / Gene: atpF, PF0181 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic References: UniProt: Q8U4A7, 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: 2.4 Å3/Da / Density % sol: 48.7 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 291 K / Method: microbatch under oil / pH: 10 Details: 40% PEG 8000, 0.1M K2CO3, 10 mM Taurine, 0.1M CAPS pH 10.0, MICROBATCH UNDER OIL, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915, 0.9795, 0.96791 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 31, 2007 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→50 Å / Num. all: 18791 / Num. obs: 18791 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 38.19 | ||||||||||||
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 13.25 / Num. unique all: 2207 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→39.8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 521149.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.3006 Å2 / ksol: 0.36129 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→39.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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