+Open data
-Basic information
Entry | Database: PDB / ID: 4ksr | ||||||
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Title | Crystal Structure of the Vibrio cholerae ATPase GspE Hexamer | ||||||
Components | Type II secretion system protein E, Hemolysin-coregulated proteinType II secretion system | ||||||
Keywords | PROTEIN TRANSPORT / T2SS secretion ATPase / EpsE / Hexamer / C2 cyclic symmetry | ||||||
Function / homology | Function and homology information protein-exporting ATPase activity / protein-secreting ATPase / protein secretion by the type II secretion system / type II protein secretion system complex / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Vibrio cholerae O1 (bacteria) Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.2 Å | ||||||
Authors | Hol, W.G. / Turley, S. / Lu, C.Y. / Park, Y.J. / Marionni, S.T. / Lee, K. / Patrick, M. / Sandkvist, M. / Bush, M. / Shah, R. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Hexamers of the Type II Secretion ATPase GspE from Vibrio cholerae with Increased ATPase Activity. Authors: Lu, C. / Turley, S. / Marionni, S.T. / Park, Y.J. / Lee, K.K. / Patrick, M. / Shah, R. / Sandkvist, M. / Bush, M.F. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ksr.cif.gz | 621.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ksr.ent.gz | 524 KB | Display | PDB format |
PDBx/mmJSON format | 4ksr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/4ksr ftp://data.pdbj.org/pub/pdb/validation_reports/ks/4ksr | 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: 64293.371 Da / Num. of mol.: 3 / Fragment: T2SS EpsE, P37093 residues 100-503, Q02UZ4 Source method: isolated from a genetically manipulated source Details: Chimeric Protein Source: (gene. exp.) Vibrio cholerae O1 (bacteria), (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961, UCBPP-PA14 / Gene: epsE, VC_2732, PA14_01030 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37093, UniProt: Q02UZ4 |
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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: 2.77 Å3/Da / Density % sol: 55.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 0.1M BisTris, 5mM ADP, 5mM MgCl2, 5mM AlCl3, 15mM NaF, 16% PEG300, 0.2M ammonium sulfate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2012 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.78→38.72 Å / Num. obs: 21927 / Rmerge(I) obs: 0.106 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 3.78→3.98 Å / % possible all: 96.8 |
-Processing
Software |
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Refinement | Resolution: 4.2→38.72 Å / Cor.coef. Fo:Fc: 0.834 / Cor.coef. Fo:Fc free: 0.831 / SU B: 265.976 / SU ML: 1.517 / Cross valid method: THROUGHOUT / ESU R Free: 1.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 136.894 Å2
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Refinement step | Cycle: LAST / Resolution: 4.2→38.72 Å
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Refine LS restraints |
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