Download MendeleyCrystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis
Dranow, D.M., Fairman, J.W., Pierce, P.G., Lorimer, D., Edwards, T.E., SSGCIDTo be published.
4YS8
Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis
- PDB DOI: https://doi.org/10.2210/pdb4YS8/pdb
- Classification: TRANSFERASE
- Organism(s): Burkholderia thailandensis E264
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2015-03-16 Released: 2015-04-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.263
- R-Value Work: 0.216
- R-Value Observed: 0.218
wwPDB Validation 3D Report Full Report
This is version 1.5 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 |
| 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | 241 | Burkholderia thailandensis E264 | Mutation(s): 0 Gene Names: ispD, BTH_I2089 EC: 2.7.7.60 |  | |
UniProt | |||||
Find proteins for Q2SWT6 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2SWT6 Go to UniProtKB: Q2SWT6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q2SWT6 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | E [auth A], F [auth A], G [auth B], I [auth C], J [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | H [auth B] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.263
- R-Value Work: 0.216
- R-Value Observed: 0.218
- Space Group: P 1 21 1
- Diffraction Data: https://doi.org/10.18430/M34YS8
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 45.65 | α = 90 |
| b = 138.31 | β = 101.89 |
| c = 78.59 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| MR-Rosetta | phasing |
Entry History
Deposition Data
- Released Date: 2015-04-01 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2015-04-01
Type: Initial release - Version 1.1: 2015-04-08
Changes: Other - Version 1.2: 2015-10-28
Changes: Database references - Version 1.3: 2017-10-11
Changes: Data collection, Derived calculations - Version 1.4: 2021-11-03
Changes: Data collection, Database references - Version 1.5: 2023-09-27
Changes: Data collection, Refinement description
