Download MendeleyCrystal structure of S-adenosyl-L-methionine methyl transferase (YP_165822.1) from SILICIBACTER POMEROYI DSS-3 at 1.80 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3IHT | pdb_00003iht
Crystal structure of S-adenosyl-L-methionine methyl transferase (YP_165822.1) from SILICIBACTER POMEROYI DSS-3 at 1.80 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3IHT/pdb
- Classification: TRANSFERASE
- Organism(s): Ruegeria pomeroyi DSS-3
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-07-30 Released: 2009-08-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.194 (Depositor), 0.200 (DCC)
- R-Value Work: 0.173 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.174 (Depositor)
This is version 1.5 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 |
| S-adenosyl-L-methionine methyl transferase | 174 | Ruegeria pomeroyi DSS-3 | Mutation(s): 0 Gene Names: SPO0562, YP_165822.1 |  | |
UniProt | |||||
Find proteins for Q5LVY3 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LVY3 Go to UniProtKB: Q5LVY3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5LVY3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SAM Query on SAM | C [auth A] | S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N |  | ||
| GOL Query on GOL | F [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| NI Query on NI | D [auth A], E [auth A] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-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: 1.80 Å
- R-Value Free: 0.194 (Depositor), 0.200 (DCC)
- R-Value Work: 0.173 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.174 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33IHT
Space Group: P 32 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 97.568 | α = 90 |
| b = 97.568 | β = 90 |
| c = 85.813 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SOLVE | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
Entry History
Deposition Data
- Released Date: 2009-08-25 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-08-25
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations - Version 1.5: 2024-10-09
Changes: Data collection, Structure summary
