[English] 日本語
![](img/lk-miru.gif)
- PDB-3luo: Crystal Structure and functional characterization of the thermoph... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3luo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure and functional characterization of the thermophilic prolyl isomerase and chaperone SlyD | ||||||
![]() |
| ||||||
![]() | ISOMERASE / PROLYL CIS TRANS ISOMERASE / CHAPERONE FUNCTION / TWO DOMAIN PROTEIN / Ni(2+) Zn(2+) BINDING / SLYD | ||||||
Function / homology | ![]() peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein refolding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Loew, C. / Neumann, P. / Weininger, U. / Stubbs, M.T. / Balbach, J. | ||||||
![]() | ![]() Title: Crystal Structure Determination and Functional Characterization of the Metallochaperone SlyD from Thermus thermophilus Authors: Loew, C. / Neumann, P. / Tidow, H. / Weininger, U. / Haupt, C. / Friedrich-Epler, B. / Scholz, C. / Stubbs, M.T. / Balbach, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 75.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 56.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 445.3 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 10.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cgmSC ![]() 3cgnC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17400.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Protein/peptide | Mass: 590.625 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE PEPTIDE SUBSTRATE WAS PURCHASED FROM A COMPANY. | ||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.58 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10MG/ML N-SUC-ALA-LEU-PRO-PHE-PNA, 2M AMMONIUM SULFATE, 5 % PEG 400, 100MM MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2009 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9841 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→20 Å / Num. all: 7658 / Num. obs: 7636 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.35 % / Biso Wilson estimate: 68.806 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.054 / Net I/σ(I): 23.77 |
Reflection shell | Resolution: 2.55→2.65 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 3.5 / Num. measured obs: 5982 / Num. unique all: 808 / Num. unique obs: 808 / Rsym value: 0.662 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CGM Resolution: 2.55→19.693 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.33 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.24 / σ(I): 0 / Stereochemistry target values: ML / Details: TLS parameters have been included in refinemnt
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 92.506 Å2 / ksol: 0.407 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 215.89 Å2 / Biso mean: 94.308 Å2 / Biso min: 31.23 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→19.693 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|