Download MendeleyThe crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritolsynthase from Anaerococcus prevotii DSM 20548
Borek, D., Tan, K., Stols, L., Eschenfeidt, W.H., Otwinoski, Z., Joachimiak, A.To be published.
4KT7
The crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritolsynthase from Anaerococcus prevotii DSM 20548
- PDB DOI: https://doi.org/10.2210/pdb4KT7/pdb
- Classification: TRANSFERASE
- Organism(s): Anaerococcus prevotii DSM 20548
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2013-05-20 Released: 2013-06-05
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.228
- R-Value Work: 0.181
- R-Value Observed: 0.183
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) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | 237 | Anaerococcus prevotii DSM 20548 | Mutation(s): 0 Gene Names: Apre_0175, ispD EC: 2.7.7.60 |  | |
UniProt | |||||
Find proteins for C7RFG6 (Anaerococcus prevotii (strain ATCC 9321 / DSM 20548 / JCM 6508 / NCTC 11806 / PC1)) Explore C7RFG6 Go to UniProtKB: C7RFG6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C7RFG6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CL Query on CL | C [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | D [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.228
- R-Value Work: 0.181
- R-Value Observed: 0.183
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 87.858 | α = 90 |
| b = 145.509 | β = 90 |
| c = 36.719 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| SHELXD | phasing |
| MLPHARE | phasing |
| DM | model building |
| ARP | model building |
| WARP | model building |
| HKL-3000 | phasing |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| DM | phasing |
| SBC-Collect | data collection |
Entry History
Deposition Data
- Released Date: 2013-06-05 Deposition Author(s): Borek, D., Tan, K., Stols, L., Eschenfeidt, W.H., Otwinoski, Z., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2013-06-05
Type: Initial release - Version 1.1: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
