Download MendeleyCrystal structure of the GTP-binding protein YchF in complexed with GDP
Kukimoto-Niino, M., Murayama, K., Shirouzu, M., Kuramitsu, S., Yokoyama, S.To be published.
2DBY
Crystal structure of the GTP-binding protein YchF in complexed with GDP
- DOI: 10.2210/pdb2DBY/pdb
- Classification: HYDROLASE
- Organism(s): Thermus thermophilus HB8
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2005-12-16 Released: 2006-06-16
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.76 Å
- R-Value Free: 0.221
- R-Value Work: 0.191
- R-Value Observed: 0.191
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| GTP-binding protein | A | 368 | Thermus thermophilus HB8 | Mutation(s): 2 Gene Names: ychF, TTHA1185 |  |
Find proteins for Q5SJ29 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)) Explore Q5SJ29 Go to UniProtKB: Q5SJ29 | |||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GDP Query on GDP | A | GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N |  | Ligand Interaction | |
| FMT Query on FMT | A | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.76 Å
- R-Value Free: 0.221
- R-Value Work: 0.191
- R-Value Observed: 0.191
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 60.384 | α = 90 |
| b = 133.169 | β = 90 |
| c = 46.432 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| SOLVE | phasing |
Entry History
Deposition Data
- Deposited Date: 2005-12-16
- Released Date: 2006-06-16 Deposition Author(s): Kukimoto-Niino, M., Murayama, K., Shirouzu, M., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
