+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ds8 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the ZBD-XB complex | ||||||
![]() |
| ||||||
![]() | METAL BINDING PROTEIN / PROTEIN BINDING / Protein-peptide complex | ||||||
Function / homology | ![]() protein denaturation / HslUV protease complex / endopeptidase Clp complex / ATP-dependent peptidase activity / protein unfolding / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / protease binding ...protein denaturation / HslUV protease complex / endopeptidase Clp complex / ATP-dependent peptidase activity / protein unfolding / proteolysis involved in protein catabolic process / ATP-dependent protein folding chaperone / disordered domain specific binding / unfolded protein binding / protease binding / protein dimerization activity / cell division / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Park, E.Y. / Lee, B.G. / Hong, S.B. / Kim, H.W. / Song, H.K. | ||||||
![]() | ![]() Title: Structural Basis of SspB-tail Recognition by the Zinc Binding Domain of ClpX. Authors: Park, E.Y. / Lee, B.G. / Hong, S.B. / Kim, H.W. / Jeon, H. / Song, H.K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 33.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 22 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 449.2 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ds5SC ![]() 2ds6C ![]() 2ds7C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 5758.631 Da / Num. of mol.: 2 / Fragment: Zinc binding domain(ZBD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 855.079 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: XB peptide (APALRVVK) is synthesized. Except the first alanine, the sequence occurs naturally in E. coli SspB #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.633 Å3/Da / Density % sol: 24.68 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M tri-sodium citrate, pH 6.5, 10-fold molar excess of XB peptide addition, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 2005 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 11450 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 64.1 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2DS5 Resolution: 1.6→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.63 Å / Rfactor Rfree error: 0.0124
|