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Open data
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Basic information
Entry | Database: PDB / ID: 2w7v | ||||||
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Title | periplasmic domain of EpsL from Vibrio parahaemolyticus | ||||||
![]() | GENERAL SECRETION PATHWAY PROTEIN L | ||||||
![]() | TRANSPORT PROTEIN / TRANSPORT / TYPE II SECRETION | ||||||
Function / homology | ![]() Gram-negative-bacterium-type cell wall / protein secretion by the type II secretion system / type II protein secretion system complex / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Abendroth, J. / Kreger, A.C. / Abendroth, H. / Sandkvist, M. / Hol, W.G.J. | ||||||
![]() | ![]() Title: The Dimer Formed by the Periplasmic Domain of Epsl from the Type 2 Secretion System of Vibrio Parahaemolyticus. Authors: Abendroth, J. / Kreger, A.C. / Hol, W.G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.3 KB | Display | ![]() |
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PDB format | ![]() | 37.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.7 KB | Display | ![]() |
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Full document | ![]() | 443.8 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.5001, 0.866, 3.0E-6), Vector: |
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Components
#1: Protein | Mass: 10911.814 Da / Num. of mol.: 2 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 319-404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | PERIPLASMIC DOMAIN SER319-GLN404, M318 IS A CLONING ARTEFACT, THE C-TERMINAL HIS6-TAG SEQUENCE ...PERIPLASMI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 51.8 % / Description: NONE |
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Crystal grow | Details: 1.2-1.4M NA/K PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 9031 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.3→39.1 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 16.714 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.242 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→39.1 Å
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Refine LS restraints |
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