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Yorodumi- PDB-2eww: Crystal Structure of the Pilus Retraction Motor PilT and Bound ATP -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eww | ||||||
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Title | Crystal Structure of the Pilus Retraction Motor PilT and Bound ATP | ||||||
Components | twitching motility protein PilT | ||||||
Keywords | PROTEIN TRANSPORT / Pilus Retraction Motor / ATPase / Hexameric PilT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å | ||||||
Authors | Satyshur, K.A. / Forest, K.T. | ||||||
Citation | Journal: Structure / Year: 2007 Title: Crystal structures of the pilus retraction motor PilT suggest large domain movements and subunit cooperation drive motility. Authors: Satyshur, K.A. / Worzalla, G.A. / Meyer, L.S. / Heiniger, E.K. / Aukema, K.G. / Misic, A.M. / Forest, K.T. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: The pilus-retraction protein PilT: ultrastructure of the biological assembly Authors: Forest, K.T. / Satyshur, K.A. / Worzalla, G.A. / Hansen, J.K. / Herdendorf, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eww.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eww.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 2eww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/2eww ftp://data.pdbj.org/pub/pdb/validation_reports/ew/2eww | 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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Details | The biological assembly is a hexamer generated from the monomer in the asymmetric unit by all six operations in P6. |
-Components
#1: Protein | Mass: 42559.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: GenBank: 15606134, UniProt: O66950*PLUS |
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#2: Chemical | ChemComp-ATP / |
#3: 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: 2.69 Å3/Da / Density % sol: 54.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: 5-8 mg/ml protein 30-45% MPD 0.2-0.4 M Ammonium Sulfate Tris, 15mM KCl 75mM 5% glycerol 5-10mM magnesium Chloride 1-5 mM ATP , pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 1, 2003 | |||||||||||||||
Radiation | Monochromator: Diamond / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.2→20 Å / Num. obs: 7481 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.9 | |||||||||||||||
Reflection shell | Resolution: 3.2→3.37 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1093 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.2→19.47 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.838 / SU B: 29.41 / SU ML: 0.499 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.642 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.716 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→19.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.203→3.284 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 20
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