Download MendeleyCrystal structures of GTP-binding protein LepA from Aquifex aeolicus.
Kawazoe, M., Takemoto, C., Kaminishi, T., Nishino, A., Nakayama-Ushikoshi, R., Hanawa-Suetsugu, K., Terada, T., Shirouzu, M., Yokoyama, S.To be published.
2YWH | pdb_00002ywh
Crystal structure of GDP-bound LepA from Aquifex aeolicus
- PDB DOI: https://doi.org/10.2210/pdb2YWH/pdb
- Classification: TRANSLATION
- Organism(s): Aquifex aeolicus VF5
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2007-04-20 Released: 2008-04-29
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.24 Å
- R-Value Free: 0.262 (Depositor), 0.250 (DCC)
- R-Value Work: 0.227 (Depositor), 0.220 (DCC)
- R-Value Observed: 0.227 (Depositor)
Starting Model: experimental
View more details
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 |
| GTP-binding protein LepA | 600 | Aquifex aeolicus VF5 | Mutation(s): 0 Gene Names: aq_1725 |  | |
UniProt | |||||
Find proteins for O67618 (Aquifex aeolicus (strain VF5)) Explore O67618 Go to UniProtKB: O67618 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O67618 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GDP Query on GDP | C [auth A] | GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N |  | ||
| MG Query on MG | B [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.24 Å
- R-Value Free: 0.262 (Depositor), 0.250 (DCC)
- R-Value Work: 0.227 (Depositor), 0.220 (DCC)
- R-Value Observed: 0.227 (Depositor)
Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 81.676 | α = 90 |
| b = 116.118 | β = 90 |
| c = 122.721 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data collection |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2008-04-29 Deposition Author(s): Kawazoe, M., Takemoto, C., Kaminishi, T., Nishino, A., Nakayama-Ushikoshi, R., Hanawa-Suetsugu, K., Terada, T., Shirouzu, M., 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: 2017-10-11
Changes: Refinement description - Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
