4II9
Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate
- PDB DOI: https://doi.org/10.2210/pdb4II9/pdb
- NAKB: 4II9
- Classification: TRANSFERASE/PEPTIDE/RNA
- Organism(s): Weissella viridescens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2012-12-20 Released: 2013-07-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.66 Å
- R-Value Free: 0.209
- R-Value Work: 0.175
- R-Value Observed: 0.177
This is version 2.1 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 |
| FemX | 343 | Weissella viridescens | Mutation(s): 0 Gene Names: femX EC: 2.3.2.10 |  | |
UniProt | |||||
Find proteins for Q9EY50 (Weissella viridescens) Explore Q9EY50 Go to UniProtKB: Q9EY50 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9EY50 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| UDP Query on UDP | E [auth B] | URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N |  | ||
| MUB Query on MUB | F [auth B] | N-acetyl-alpha-muramic acid C11 H19 N O8 MNLRQHMNZILYPY-MDMHTWEWSA-N |  | ||
| GOL Query on GOL | D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.66 Å
- R-Value Free: 0.209
- R-Value Work: 0.175
- R-Value Observed: 0.177
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 42.13 | α = 90 |
| b = 101.77 | β = 102.6 |
| c = 46.32 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MX | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
Entry History
Deposition Data
- Released Date: 2013-07-03 Deposition Author(s): Li de la Sierra-Gallay, I., Fonvielle, M., van Tilbeurgh, H., Arthur, M., Etheve-Quelquejeu, M.
Revision History (Full details and data files)
- Version 1.0: 2013-07-03
Type: Initial release - Version 1.1: 2013-08-07
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
