Download MendeleyCrystal Structure of tryptophanyl-tRNA synthetase from Mycoplasma pneumoniae
Ishii, T., Bessho, Y., Yokoyama, S.To be published.
2YY5
Crystal Structure of tryptophanyl-tRNA synthetase from Mycoplasma pneumoniae
- PDB DOI: https://doi.org/10.2210/pdb2YY5/pdb
- Classification: LIGASE
- Organism(s): Mycoplasmoides pneumoniae M129
- Mutation(s): Yes
- Deposited: 2007-04-27 Released: 2008-04-29
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.251
- R-Value Work: 0.192
- R-Value Observed: 0.192
Starting Model: experimental
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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 | 348 | Mycoplasmoides pneumoniae M129 | Mutation(s): 1 EC: 6.1.1.2 |  | |
UniProt | |||||
Find proteins for P75510 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)) Explore P75510 Go to UniProtKB: P75510 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P75510 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| WSA Query on WSA | G [auth A], J [auth B], M [auth C], P [auth D] | 5'-O-[(L-TRYPTOPHYLAMINO)SULFONYL]ADENOSINE C21 H24 N8 O7 S RQAVKMXDGHWLGD-BFNSABJLSA-N |  | ||
| SO4 Query on SO4 | E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.55 Å
- R-Value Free: 0.251
- R-Value Work: 0.192
- R-Value Observed: 0.192
- Space Group: P 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 88.163 | α = 90 |
| b = 52.109 | β = 96.05 |
| c = 194.092 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2008-04-29 Deposition Author(s): Ishii, T., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2008-04-29
Type: Initial release - Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 1.2: 2021-11-10
Changes: Database references, Derived calculations - Version 1.3: 2023-10-25
Changes: Data collection, Refinement description
