[English] 日本語
![](img/lk-miru.gif)
- PDB-4g4i: Crystal structure of glucuronoyl esterase S213A mutant from Sporo... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4g4i | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of glucuronoyl esterase S213A mutant from Sporotrichum thermophile determined at 1.9 A resolution | ||||||
![]() | 4-O-methyl-glucuronoyl methylesterase | ||||||
![]() | HYDROLASE / Alpha/Beta Hydrolase / 3-layer alpha/beta/alpha sandwich / Rossmann Fold / Glucuronoyl esterase | ||||||
Function / homology | ![]() (4-O-methyl)-D-glucuronate-lignin esterase / lignin catabolic process / carboxylic ester hydrolase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Charvagi, M.D. / Dimarogona, M. / Topakas, E. / Christakopoulos, P. / Chrysina, E.D. | ||||||
![]() | ![]() Title: The structure of a novel glucuronoyl esterase from Myceliophthora thermophila gives new insights into its role as a potential biocatalyst. Authors: Charavgi, M.D. / Dimarogona, M. / Topakas, E. / Christakopoulos, P. / Chrysina, E.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 95.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 69.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 452.4 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 30.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4g4gSC ![]() 4g4jC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 46046.168 Da / Num. of mol.: 1 / Mutation: S213A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: G2QJR6, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THIS SEGMENT CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.33 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 25% PEG 550 MME, 0.1M sodium acetate , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 1.5419 Å |
Detector | Type: Atlas 135mm CCD detector / Detector: CCD / Date: Nov 11, 2011 / Details: Mutlti-layer Xray optic |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→13.97 Å / Num. all: 30113 / Num. obs: 30113 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3 / Num. unique all: 4161 / % possible all: 95.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4G4G Resolution: 1.9→13.93 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.827 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.199 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.186 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→13.93 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.948 Å / Total num. of bins used: 20
|