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Download EndnoteCrystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal
Manoj Kumar, P., Baskar, V., Manicka, S., Krishnaswamy, S.To be published.
4OE7
Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal
- DOI: 10.2210/pdb4OE7/pdb
- Classification: LYASE
- Organism(s): Escherichia coli K-12
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2014-01-12 Released: 2014-12-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.99 Å
- R-Value Free: 0.233
- R-Value Work: 0.198
- R-Value Observed: 0.200
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Probable 2-keto-3-deoxy-galactonate aldolase YagE | A, B, C, D | 343 | Escherichia coli K-12 | Mutation(s): 0 Gene Names: b0268, JW0261, yagE EC: 4.1.2 (PDB Primary Data), 4.1.2.51 (UniProt), 4.1.2.28 (UniProt) |  |
Find proteins for P75682 (Escherichia coli (strain K12)) Explore P75682 Go to UniProtKB: P75682 | |||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 7 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GXP Query on GXP | B, D | (4S)-4-hydroxy-2,5-dioxopentanoic acid C5 H6 O5 QZKCWTOLHHFWCD-VKHMYHEASA-N |  | Ligand Interaction | |
| GXS Query on GXS | B, D | (4R)-4-hydroxy-2,5-dioxopentanoic acid C5 H6 O5 QZKCWTOLHHFWCD-GSVOUGTGSA-N |  | Ligand Interaction | |
| GOL Query on GOL | A, B, C, D | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| PYR Query on PYR | A, C | PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N |  | Ligand Interaction | |
| EDO Query on EDO | A, B, C, D | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| GXT Query on GXT | A | ethanedial C2 H2 O2 LEQAOMBKQFMDFZ-UHFFFAOYSA-N |  | Ligand Interaction | |
| MG Query on MG | A, B, C, D | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.99 Å
- R-Value Free: 0.233
- R-Value Work: 0.198
- R-Value Observed: 0.200
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 141.24 | α = 90 |
| b = 155.14 | β = 90 |
| c = 55.58 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHASER | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
Entry History
Deposition Data
- Deposited Date: 2014-01-12
- Released Date: 2014-12-24 Deposition Author(s): Manoj Kumar, P., Baskar, V., Manicka, S., Krishnaswamy, S.
