[English] 日本語
![](img/lk-miru.gif)
- PDB-4erg: Evidence for a Dual Role of an Active Site Histidine in alpha-Ami... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4erg | ||||||
---|---|---|---|---|---|---|---|
Title | Evidence for a Dual Role of an Active Site Histidine in alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde Decarboxylase | ||||||
![]() | 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase | ||||||
![]() | LYASE / tim-barrel / decarboxylase / metal-binding / Fe | ||||||
Function / homology | ![]() secondary metabolic process / : / : / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huo, L. / Fielding, A.J. / Chen, Y. / Li, T. / Iwaki, H. / Hosler, J.P. / Chen, L. / Hasegawa, Y. / Que Jr., L. / Liu, A. | ||||||
![]() | ![]() Title: Evidence for a Dual Role of an Active Site Histidine in alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde Decarboxylase Authors: Huo, L. / Fielding, A.J. / Chen, Y. / Li, T. / Iwaki, H. / Hosler, J.P. / Chen, L. / Hasegawa, Y. / Que, L. / Liu, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 139.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 109.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444.8 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4epkC ![]() 4eraC ![]() 4eriC ![]() 2hbxS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37208.621 Da / Num. of mol.: 2 / Mutation: H228Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.54 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 17% PEG 5000, 0.1M Tris, 0.2 M MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.789→83.77 Å / Num. all: 18046 / Num. obs: 18010 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 24.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 60.8 |
Reflection shell | Resolution: 2.789→2.85 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2.49 / Num. unique all: 879 / % possible all: 99.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2HBX Resolution: 2.789→83.77 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.915 / SU B: 19.436 / SU ML: 0.386 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.429 / 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: 86.192 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.789→83.77 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.789→2.862 Å / Total num. of bins used: 20
|