[English] 日本語
![](img/lk-miru.gif)
- PDB-1ks4: The structure of Aspergillus niger endoglucanase-palladium complex -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ks4 | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of Aspergillus niger endoglucanase-palladium complex | ||||||
![]() | Endoglucanase A | ||||||
![]() | HYDROLASE / Endoglucanase / Cellulase / Aspergillus niger / family 9 / (alpha/alpha)6 | ||||||
Function / homology | ![]() cellulase / cellulase activity / polysaccharide catabolic process / transferase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Khademi, S. / Zhang, D. / Swanson, S.M. / Wartenberg, A. / Witte, C. / Meyer, E.F. | ||||||
![]() | ![]() Title: Determination of the structure of an endoglucanase from Aspergillus niger and its mode of inhibition by palladium chloride. Authors: Khademi, S. / Zhang, D. / Swanson, S.M. / Wartenberg, A. / Witte, K. / Meyer, E.F. | ||||||
History |
| ||||||
Remark 650 | HELIX AUTHOR PROVIDED HELIX RECORDS | ||||||
Remark 700 | SHEET AUTHOR PROVIDED SHEET RECORDS |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 52.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 41 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 418.4 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 13.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 24283.145 Da / Num. of mol.: 1 / Fragment: Aspergillus niger Endoglucanase / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.36 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: PEG 4000, Sodium Acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAC Science DIP-2030K / Detector: IMAGE PLATE / Date: Oct 1, 1994 / Details: mirrors |
Radiation | Monochromator: Osmic, Model 140-000023 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 11142 / Num. obs: 10691 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 2.5→2.55 Å / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 3.7 / % possible all: 89.5 |
Reflection | *PLUS Num. obs: 11084 / Num. measured all: 117527 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 89.3 % / Rmerge(I) obs: 0.63 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.743 Å2 / ksol: 0.339 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.242 / Rfactor Rwork: 0.208 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|