[English] 日本語
![](img/lk-miru.gif)
- PDB-5nzi: Crystal structure of UDP-glucose pyrophosphorylase S374F mutant f... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5nzi | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of UDP-glucose pyrophosphorylase S374F mutant from Leishmania major in complex with UDP-glucose | ||||||
![]() | UDP-glucose pyrophosphorylase | ||||||
![]() | TRANSFERASE / NTP-transferase / Pathogen / Allostery / Catalysis | ||||||
Function / homology | ![]() UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / nuclear lumen / ciliary plasm / glycogen metabolic process / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cramer, J.T. / Fuehring, J.I. / Baruch, P. / Bruetting, C. / Hesse, R. / Knoelker, H.-J. / Gerardy-Schahn, R. / Fedorov, R. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Decoding Allosteric Networks in Biocatalysts: Rational Approach to Therapies and Biotechnologies Authors: Cramer, J.T. / Fuehring, J.I. / Baruch, P. / Bruetting, C. / Knoelker, H.-J. / Gerardy-Schahn, R. / Fedorov, R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 207.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 166.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 827.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 837.6 KB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 30.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nzgC ![]() 5nzhC ![]() 5nzjC ![]() 5nzkC ![]() 5nzlC ![]() 5nzmC ![]() 2m2aS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 56114.863 Da / Num. of mol.: 1 / Mutation: S374F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q4QDU3, UTP-glucose-1-phosphate uridylyltransferase | ||
---|---|---|---|
#2: Chemical | ChemComp-UPG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.08 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 24% PEG 3350, 100 mM Bis-Tris pH 6.8, 0.2 M Li2SO4, 2 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 30193 / % possible obs: 98.5 % / Redundancy: 13.43 % / Rsym value: 0.055 / Net I/σ(I): 10.49 |
Reflection shell | Resolution: 2.05→2.15 Å / Mean I/σ(I) obs: 2.24 / Num. unique all: 3929 / Rsym value: 0.421 / % possible all: 97.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2M2A Resolution: 2.05→44.756 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.74 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→44.756 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|