Download MendeleyCrystal structure of tryptophanyl-tRNA synthetase from hyperthermophilic archaeon, Aeropyrum pernix K1
Tsuchiya, W., Fujimoto, Z., Hasegawa, T.To be published.
3A04
Crystal structure of tryptophanyl-tRNA synthetase from hyperthermophilic archaeon, Aeropyrum pernix K1
- PDB DOI: https://doi.org/10.2210/pdb3A04/pdb
- Classification: LIGASE
- Organism(s): Aeropyrum pernix
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-03-02 Released: 2010-03-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.97 Å
- R-Value Free: 0.235
- R-Value Work: 0.178
- R-Value Observed: 0.180
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 |
| Tryptophanyl-tRNA synthetase | 372 | Aeropyrum pernix | Mutation(s): 0 Gene Names: trpS, APE_2461.1 EC: 6.1.1.2 |  | |
UniProt | |||||
Find proteins for Q9Y924 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9Y924 Go to UniProtKB: Q9Y924 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9Y924 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SF4 Query on SF4 | B [auth A] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N |  | ||
| CD Query on CD | C [auth A], D [auth A] | CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.97 Å
- R-Value Free: 0.235
- R-Value Work: 0.178
- R-Value Observed: 0.180
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 98.709 | α = 90 |
| b = 103.194 | β = 90 |
| c = 97.806 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2010-03-09 Deposition Author(s): Tsuchiya, W., Fujimoto, Z., Hasegawa, T.
Revision History (Full details and data files)
- Version 1.0: 2010-03-09
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations - Version 1.3: 2024-04-03
Changes: Refinement description
