[English] 日本語
![](img/lk-miru.gif)
- PDB-2vma: The three-dimensional structure of the cytoplasmic domains of Eps... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2vma | ||||||
---|---|---|---|---|---|---|---|
Title | The three-dimensional structure of the cytoplasmic domains of EpsF from the Type 2 Secretion System of Vibrio cholerae | ||||||
![]() | GENERAL SECRETION PATHWAY PROTEIN F | ||||||
![]() | TRANSPORT PROTEIN / TRANSMEMBRANE / INNER MEMBRANE / TYPE 2 SECRETION / T4PB / T2SS / VIBRIO / CHOLERA / MEMBRANE / TRANSPORT / PROTEIN SECRETION | ||||||
Function / homology | ![]() protein secretion by the type II secretion system / type II protein secretion system complex / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Abendroth, J. / Korotkov, K.V. / Mitchell, D.D. / Kreger, A. / Hol, W.G.J. | ||||||
![]() | ![]() Title: The Three-Dimensional Structure of the Cytoplasmic Domains of Epsf from the Type 2 Secretion System of Vibrio Cholerae. Authors: Abendroth, J. / Mitchell, D.D. / Korotkov, K.V. / Johnson, T.L. / Kreger, A. / Sandkvist, M. / Hol, W.G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 62.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 437.8 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||||||||
2 | ![]()
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.99988, 0.00497, -0.01461), Vector: |
-
Components
#1: Protein | Mass: 14028.238 Da / Num. of mol.: 2 / Fragment: RESIDUES 56-170 Source method: isolated from a genetically manipulated source Details: RESIDUES 56-170, PLUS C-TERMINAL TEV- CLEAVABLE HIS6-TAG Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-IOD / #4: Water | ChemComp-HOH / | Sequence details | CYTOPLASMI | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.08 % / Description: NONE |
---|---|
Crystal grow | pH: 7 Details: 1UL PROTEIN, 1UL RESERVOIR: 12.5% PEG 400, 200MM CAOAC2, 100MM MES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Oct 23, 2006 / Details: MIRRORS |
Radiation | Monochromator: OSMIC VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.82 Å / Num. obs: 18609 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 12.11 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.9 / % possible all: 77.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.9→46.32 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.078 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 17.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|