3IC3
Structure of a putative pyruvate dehydrogenase from the photosynthetic bacterium Rhodopseudomonas palustrus CGA009
- PDB DOI: https://doi.org/10.2210/pdb3IC3/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Rhodopseudomonas palustris
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-07-17 Released: 2009-09-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.195
- R-Value Work: 0.167
- R-Value Observed: 0.168
This is version 1.3 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| putative pyruvate dehydrogenase | 101 | Rhodopseudomonas palustris | Mutation(s): 0 Gene Names: JGI_07::RPA2865, RPA2865 |  | |
UniProt | |||||
Find proteins for Q6N5V5 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N5V5 Go to UniProtKB: Q6N5V5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6N5V5 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| BGC Query on BGC | G [auth B] | beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N |  | ||
| PO4 Query on PO4 | J [auth C], L [auth D], M [auth D] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| EDO Query on EDO | E [auth A], F [auth A], I [auth B], N [auth D] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| K Query on K | H [auth B] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N |  | ||
| NA Query on NA | K [auth C] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| 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: 1.80 Å
- R-Value Free: 0.195
- R-Value Work: 0.167
- R-Value Observed: 0.168
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 64.7 | α = 90 |
| b = 64.995 | β = 90 |
| c = 116.89 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MLPHARE | phasing |
| DM | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| SHELXD | phasing |
| SHELXE | model building |
| SOLVE | phasing |
| RESOLVE | phasing |
| ARP/wARP | model building |
| CCP4 | phasing |
| O | model building |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2009-09-22 Deposition Author(s): Cuff, M.E., Tesar, C., Jedrzejczak, R., Mckinlay, J.B., Harwood, C.S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-09-22
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
