+
Open data
-
Basic information
Entry | Database: PDB / ID: 1eua | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SCHIFF BASE INTERMEDIATE IN KDPG ALDOLASE FROM ESCHERICHIA COLI | |||||||||
![]() | KDPG ALDOLASE | |||||||||
![]() | LYASE / BETA BARREL / TRIMER / CARBINOLAMINE | |||||||||
Function / homology | ![]() (4S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-2-oxoglutarate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase / oxo-acid-lyase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / oxaloacetate decarboxylase activity / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / metabolic process / identical protein binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Allard, J. / Grochulski, P. / Sygusch, J. | |||||||||
![]() | ![]() Title: Covalent intermediate trapped in 2-keto-3-deoxy-6- phosphogluconate (KDPG) aldolase structure at 1.95-A resolution. Authors: Allard, J. / Grochulski, P. / Sygusch, J. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 142.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 111.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 461.9 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 22304.951 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P0A955, UniProt: A0A140NB38*PLUS, 2-dehydro-3-deoxy-phosphogluconate aldolase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.97 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, ammonium sulfate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 190 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→99 Å / Num. all: 45706 / Num. obs: 44409 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Biso Wilson estimate: 17.2 Å2 / Limit h max: 27 / Limit h min: 0 / Limit k max: 43 / Limit k min: 0 / Limit l max: 68 / Limit l min: 0 / Observed criterion F max: 601772.91 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.087 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.94 % / Rmerge(I) obs: 0.293 / % possible all: 92.2 |
Reflection | *PLUS % possible obs: 99.4 % |
Reflection shell | *PLUS % possible obs: 92.2 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.95→50.37 Å / Occupancy max: 1 / Occupancy min: 0.8 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 51.5349 Å2 / ksol: 0.362848 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.92 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→50.37 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.243 / Rfactor Rwork: 0.201 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|