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Yorodumi- PDB-2d2f: Crystal structure of atypical cytoplasmic ABC-ATPase SufC from Th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d2f | ||||||
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Title | Crystal structure of atypical cytoplasmic ABC-ATPase SufC from Thermus thermophilus HB8 | ||||||
Components | SufC protein | ||||||
Keywords | PROTEIN BINDING / ABC-ATPase / Suf protein / 310-helix / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Watanabe, S. / Kita, A. / Miki, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal Structure of Atypical Cytoplasmic ABC-ATPase SufC from Thermus thermophilus HB8. Authors: Watanabe, S. / Kita, A. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d2f.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d2f.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 2d2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/2d2f ftp://data.pdbj.org/pub/pdb/validation_reports/d2/2d2f | 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
#1: Protein | Mass: 27605.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SH92 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ADP / | #4: Chemical | #5: 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: 2.08 Å3/Da / Density % sol: 40.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6 Details: 0.1M Tris, 15% PEG 4000, 150mM MgCl2, 20% glycerol, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 2, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 17827 / Num. obs: 17807 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.2 Å2 / Rsym value: 0.057 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.246 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.87 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 980145.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.5295 Å2 / ksol: 0.367351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→39.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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