[English] 日本語
![](img/lk-miru.gif)
- PDB-1ec8: E. COLI GLUCARATE DEHYDRATASE BOUND TO PRODUCT 2,3-DIHYDROXY-5-OX... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ec8 | ||||||
---|---|---|---|---|---|---|---|
Title | E. COLI GLUCARATE DEHYDRATASE BOUND TO PRODUCT 2,3-DIHYDROXY-5-OXO-HEXANEDIOATE | ||||||
![]() | GLUCARATE DEHYDRATASE | ||||||
![]() | LYASE / Glucarate Dehydratase Enolase Enzyme Superfamily TIM Barrel (beta/alpha)7beta barrel | ||||||
Function / homology | ![]() glucarate dehydratase activity / D-glucarate catabolic process / glucarate dehydratase / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gulick, A.M. / Hubbard, B.K. / Gerlt, J.A. / Rayment, I. | ||||||
![]() | ![]() Title: Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli. Authors: Gulick, A.M. / Hubbard, B.K. / Gerlt, J.A. / Rayment, I. #1: ![]() Title: Evolution of Enzymative Activities in the Enolase Superfamily: Crystal Structure of (D)-glucarate Dehydratase from Pseudomonas putida Authors: Gulick, A.M. / Palmer, D.R. / Babbitt, P.C. / Gerlt, J.A. / Rayment, I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 373.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 299.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 546.3 KB | Display | |
Data in XML | ![]() | 81.2 KB | Display | |
Data in CIF | ![]() | 116.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 49196.855 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P76637, UniProt: P0AES2*PLUS, glucarate dehydratase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-GLR / #4: Chemical | ChemComp-IPA / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.74 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: microbatch / pH: 8 Details: 1:1 mixture of protein and 14 % PEG5000 Monomethylether 75 mM MgCl2 5 % isopropanol 50 mM Hepps , pH 8.0, microbatch, temperature 4.0K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 53 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / Details: used microseeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: OTHER / Detector: CCD / Date: Feb 11, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 675032 / Num. obs: 656955 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.159 / Num. unique all: 21149 / % possible all: 93.3 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 152351 / % possible obs: 96.2 % / Num. measured all: 675032 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 93.3 % / Rmerge(I) obs: 0.182 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.9→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: TNT Least squares refinement
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / σ(F): 0 / Rfactor all: 0.196 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|