[English] 日本語
![](img/lk-miru.gif)
- PDB-5zci: Crystal structure of apo form of Xylose reductase from Debaryomyc... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5zci | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of apo form of Xylose reductase from Debaryomyces nepalensis | ||||||
![]() | Aldose reductase | ||||||
![]() | OXIDOREDUCTASE / carbohydrate metabolism / aldo-keto reductase / TIM barrel / NADPH dependent | ||||||
Function / homology | ![]() D-xylose reductase [NAD(P)H] / D-xylose reductase (NADPH) activity / D-xylose catabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Manoj, N. | ||||||
![]() | ![]() Title: Crystal structure of yeast xylose reductase in complex with a novel NADP-DTT adduct provides insights into substrate recognition and catalysis. Authors: Paidimuddala, B. / Mohapatra, S.B. / Gummadi, S.N. / Manoj, N. #1: ![]() Title: A halotolerant aldose reductase from Debaryomyces nepalensis: gene isolation, overexpression and biochemical characterization Authors: Paidimuddala, B. / Aradhyam, G.K. / Gummadi, S.N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 246.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 197.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 434.8 KB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 38.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zcmC ![]() 1jezS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38920.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.1 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 24% PEG 3000, 0.1 M sodium citrate (pH 6.2), 0.15 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 3, 2016 |
Radiation | Monochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→52.4 Å / Num. obs: 42060 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.049 / Rrim(I) all: 0.165 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5483 / CC1/2: 0.779 / Rpim(I) all: 0.232 / Rrim(I) all: 0.781 / % possible all: 81.1 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1JEZ Resolution: 2→48.857 Å / SU ML: 0.22 / SU R Cruickshank DPI: 0.224 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.74
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.2 Å2 | ||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.238 Å / Luzzati d res low obs: 48.9 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→48.857 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.047 Å
|