Download MendeleyCrystal structure of NAD-binding 6-phosphogluconate dehydrogenase from Dyadobacter fermentans
Michalska, K., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)To be published.
4GBJ
Crystal structure of NAD-binding 6-phosphogluconate dehydrogenase from Dyadobacter fermentans
- PDB DOI: https://doi.org/10.2210/pdb4GBJ/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Dyadobacter fermentans DSM 18053
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2012-07-27 Released: 2012-09-05
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.197
- R-Value Work: 0.160
- R-Value Observed: 0.161
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 6-phosphogluconate dehydrogenase NAD-binding | A, B, C, D | 297 | Dyadobacter fermentans DSM 18053 | Mutation(s): 0 Gene Names: Dfer_3638 |  |
UniProt | |||||
Find proteins for C6VV20 (Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / CIP 107007 / KCTC 52180 / NS114)) Explore C6VV20 Go to UniProtKB: C6VV20 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C6VV20 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NA Query on NA | E [auth B], F [auth C], G [auth C], H [auth D] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 Å
- R-Value Free: 0.197
- R-Value Work: 0.160
- R-Value Observed: 0.161
- Space Group: P 21 21 21
- Diffraction Data: https://doi.org/10.18430/M34GBJ
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 79.633 | α = 90 |
| b = 89.645 | β = 90 |
| c = 151.506 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| SHELX | model building |
| MLPHARE | phasing |
| DM | model building |
| BUCCANEER | model building |
| Coot | model building |
| BUSTER | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| SHELX | phasing |
| DM | phasing |
| BUCCANEER | phasing |
Entry History
Deposition Data
- Released Date: 2012-09-05 Deposition Author(s): Michalska, K., Holowicki, J., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2012-09-05
Type: Initial release
