Download MendeleyThe Crystal Structure of a Putative Phenylalanyl-tRNA synthetase (PheRS) beta chain domain from Bacteroides fragilis to 2.1A
Stein, A.J., Sather, A., Hendricks, R., Keigher, L., Joachimiak, A.To be published.
3IG2 | pdb_00003ig2
The Crystal Structure of a Putative Phenylalanyl-tRNA synthetase (PheRS) beta chain domain from Bacteroides fragilis to 2.1A
- PDB DOI: https://doi.org/10.2210/pdb3IG2/pdb
- Classification: LIGASE
- Organism(s): Bacteroides fragilis
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-07-27 Released: 2009-09-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.09 Å
- R-Value Free: 0.236 (Depositor), 0.250 (DCC)
- R-Value Work: 0.195 (Depositor), 0.216 (DCC)
- R-Value Observed: 0.197 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| Phenylalanyl-tRNA synthetase beta chain | 213 | Bacteroides fragilis | Mutation(s): 0 Gene Names: BF2565, BF2590, pheT EC: 6.1.1.20 |  | |
UniProt | |||||
Find proteins for Q5LC76 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LC76 Go to UniProtKB: Q5LC76 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5LC76 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MG Query on MG | E [auth C] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.09 Å
- R-Value Free: 0.236 (Depositor), 0.250 (DCC)
- R-Value Work: 0.195 (Depositor), 0.216 (DCC)
- R-Value Observed: 0.197 (Depositor)
Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 48.496 | α = 99.04 |
| b = 60.335 | β = 100.37 |
| c = 78.805 | γ = 105.08 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| SHELX | phasing |
| MLPHARE | phasing |
| DM | phasing |
| ARP/wARP | model building |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2009-09-01 Deposition Author(s): Stein, A.J., Sather, A., Hendricks, R., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-09-01
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary
