- PDB-4ksr: Crystal Structure of the Vibrio cholerae ATPase GspE Hexamer -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4ksr
Title
Crystal Structure of the Vibrio cholerae ATPase GspE Hexamer
Components
Type II secretion system protein E, Hemolysin-coregulated protein
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
Type II secretion system protein GspE / Type II secretion system protein GspE, N-terminal superfamily / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
A: Type II secretion system protein E, Hemolysin-coregulated protein B: Type II secretion system protein E, Hemolysin-coregulated protein C: Type II secretion system protein E, Hemolysin-coregulated protein
A: Type II secretion system protein E, Hemolysin-coregulated protein B: Type II secretion system protein E, Hemolysin-coregulated protein C: Type II secretion system protein E, Hemolysin-coregulated protein
A: Type II secretion system protein E, Hemolysin-coregulated protein B: Type II secretion system protein E, Hemolysin-coregulated protein C: Type II secretion system protein E, Hemolysin-coregulated protein
TypeIIsecretionsystemproteinE, Hemolysin-coregulatedprotein / T2SS protein E / Cholera toxin secretion protein EpsE / General secretion pathway protein E / Type ...T2SS protein E / Cholera toxin secretion protein EpsE / General secretion pathway protein E / Type II traffic warden ATPase
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
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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 %
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
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Processing
Software
Name
Version
Classification
NB
XSCALE
datascaling
REFMAC
refinement
PDB_EXTRACT
3.11
dataextraction
XDS
datascaling
PHASES
phasing
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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.37624
829
5.2 %
RANDOM
Rwork
0.38437
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obs
0.38393
15196
98.78 %
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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