Download MendeleyStructures of Fully-Folded Native and Partially-Folded Intermediate States of Peptidyl-tRNA Hydrolase from Mycobacterium smegmatis
Kumar, A., Singh, N., Yadav, R., Sharma, S., Arora, A., Singh, T.P.To be published.
3KK0
Crystal structure of partially folded intermediate state of peptidyl-tRNA hydrolase from Mycobacterium smegmatis
- PDB DOI: https://doi.org/10.2210/pdb3KK0/pdb
- Classification: HYDROLASE
- Organism(s): Mycolicibacterium smegmatis MC2 155
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-11-04 Released: 2010-11-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.241
- R-Value Work: 0.223
- R-Value Observed: 0.237
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) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Peptidyl-tRNA hydrolase | 191 | Mycolicibacterium smegmatis MC2 155 | Mutation(s): 0 EC: 3.1.1.29 |  | |
UniProt | |||||
Find proteins for A0R3D3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R3D3 Go to UniProtKB: A0R3D3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0R3D3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PEG Query on PEG | I [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| BME Query on BME | J [auth A] | BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | E [auth A], F [auth A], G [auth A], H [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| IPA Query on IPA | B [auth A], C [auth A], D [auth A] | ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.241
- R-Value Work: 0.223
- R-Value Observed: 0.237
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.006 | α = 90 |
| b = 65.597 | β = 90 |
| c = 68.69 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MAR345dtb | data collection |
| AMoRE | phasing |
| CNS | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2010-11-10 Deposition Author(s): Kumar, A., Singh, N., Yadav, R., Sharma, S., Arora, A., Singh, T.P.
Revision History (Full details and data files)
- Version 1.0: 2010-11-10
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
