[English] 日本語
![](img/lk-miru.gif)
- PDB-4hu9: E. coli thioredoxin variant with (4S)-FluoroPro76 as single proli... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4hu9 | ||||||
---|---|---|---|---|---|---|---|
Title | E. coli thioredoxin variant with (4S)-FluoroPro76 as single proline residue | ||||||
![]() | Thioredoxin-1 | ||||||
![]() | OXIDOREDUCTASE / 4s-fluoroproline / cisproline / thioredoxin fold / protein disulfide oxidoreductase activity | ||||||
Function / homology | ![]() DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Scharer, M.A. / Rubini, M. / Capitani, G. / Glockshuber, R. | ||||||
![]() | ![]() Title: (4R)- and (4S)-Fluoroproline in the Conserved cis-Prolyl Peptide Bond of the Thioredoxin Fold: Tertiary Structure Context Dictates Ring Puckering. Authors: Rubini, M. / Scharer, M.A. / Capitani, G. / Glockshuber, R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 55.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 42.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 410.4 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 11601.229 Da / Num. of mol.: 1 / Mutation: P34A, P40A, P64A, P68A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-CU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.06 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 20 mM acetic acid-NaOH, 2 mM CuCl2, 30 % (v/v) MPD, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 18, 2012 / Details: Mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 124014 / Rmerge(I) obs: 0.192 / D res high: 1.55 Å / Num. obs: 19020 / % possible obs: 99.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→43.18 Å / Num. obs: 19020 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.005 Å2 / Rmerge(I) obs: 0.192 / Net I/σ(I): 6.92 |
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 39.63 Å2 / Biso mean: 10.6739 Å2 / Biso min: 1.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→43.181 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
|