Download MendeleyCrystal Structure of a radical SAM methyltransferase from Sphaerobacter thermophilus
Shaw, J.M., Hinchliffe, P., Spencer, J.To be published.
6FZ6 | pdb_00006fz6
Crystal Structure of a radical SAM methyltransferase from Sphaerobacter thermophilus
- PDB DOI: https://doi.org/10.2210/pdb6FZ6/pdb
- Classification: TRANSFERASE
- Organism(s): Sphaerobacter thermophilus DSM 20745
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2018-03-14 Released: 2019-04-10
- Funding Organization(s): Biotechnology and Biological Sciences Research Council
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.42 Å
- R-Value Free: 0.187 (Depositor), 0.185 (DCC)
- R-Value Work: 0.166 (Depositor), 0.165 (DCC)
- R-Value Observed: 0.167 (Depositor)
This is version 1.1 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 dual-specificity RNA methyltransferase RlmN | 366 | Sphaerobacter thermophilus DSM 20745 | Mutation(s): 0 Gene Names: rlmN, Sthe_1821 EC: 2.1.1.192 |  | |
UniProt | |||||
Find proteins for D1C4T7 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C4T7 Go to UniProtKB: D1C4T7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D1C4T7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SAH Query on SAH | D [auth A], H [auth B] | S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N |  | ||
| SF4 Query on SF4 | C [auth A], G [auth B] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | E [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| BR Query on BR | F [auth A], I [auth B] | BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| SMC Query on SMC | A, B | L-PEPTIDE LINKING | C4 H9 N O2 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.42 Å
- R-Value Free: 0.187 (Depositor), 0.185 (DCC)
- R-Value Work: 0.166 (Depositor), 0.165 (DCC)
- R-Value Observed: 0.167 (Depositor)
Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 131.84 | α = 90 |
| b = 53.14 | β = 90 |
| c = 113.57 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
| AutoSol | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-04-10 Deposition Author(s): Hinchliffe, P., Shaw, J.M., Spencer, J.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Biotechnology and Biological Sciences Research Council | United Kingdom | BB/J017906/1 |
| Biotechnology and Biological Sciences Research Council | United Kingdom | BB/M012107/1 |
Revision History (Full details and data files)
- Version 1.0: 2019-04-10
Type: Initial release - Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary
