Download MendeleyCrystal structure of probable rRNA-methyltransferase from Porphyromonas gingivalis
Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.To be published.
3KW2
Crystal structure of probable rRNA-methyltransferase from Porphyromonas gingivalis
- PDB DOI: https://doi.org/10.2210/pdb3KW2/pdb
- Classification: TRANSFERASE
- Organism(s): Porphyromonas gingivalis ATCC 33277
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-11-30 Released: 2010-01-19
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.266
- R-Value Work: 0.210
- R-Value Observed: 0.213
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 |
| Probable r-RNA methyltransferase | 257 | Porphyromonas gingivalis ATCC 33277 | Mutation(s): 0 Gene Names: PGN_0201 |  | |
UniProt | |||||
Find proteins for B2RH75 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561)) Explore B2RH75 Go to UniProtKB: B2RH75 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B2RH75 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ADN Query on ADN | C [auth A], D [auth B] | ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.266
- R-Value Work: 0.210
- R-Value Observed: 0.213
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 40.565 | α = 90 |
| b = 100.86 | β = 90 |
| c = 119.634 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| CBASS | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHENIX | phasing |
Entry History
Deposition Data
- Released Date: 2010-01-19 Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2010-01-19
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
