Download MendeleyThe structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 in complex with Selenomethionine.
Cuff, M.E., Li, H., Hatzos-Skintges, C., Tesar, C., Bearden, J., Clancy, A., Joachimiak, A.To be published.
3RPD
The structure of a B12-independent methionine synthase from Shewanella sp. W3-18-1 in complex with Selenomethionine.
- PDB DOI: https://doi.org/10.2210/pdb3RPD/pdb
- Classification: TRANSFERASE
- Organism(s): Shewanella sp. W3-18-1
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2011-04-26 Released: 2011-08-31
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.189
- R-Value Work: 0.164
- R-Value Observed: 0.165
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 |
| Methionine synthase (B12-independent) | 357 | Shewanella sp. W3-18-1 | Mutation(s): 0 Gene Names: Sputw3181_1250 EC: 2.1.1.14 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MSE Query on MSE | D [auth A], G [auth B] | SELENOMETHIONINE C5 H11 N O2 Se RJFAYQIBOAGBLC-BYPYZUCNSA-N |  | ||
| GOL Query on GOL | E [auth A], H [auth B], I [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | C [auth A], F [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-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: 1.50 Å
- R-Value Free: 0.189
- R-Value Work: 0.164
- R-Value Observed: 0.165
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 46.099 | α = 90 |
| b = 89.371 | β = 92.45 |
| c = 86.526 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MLPHARE | phasing |
| DM | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| SHELXD | phasing |
| SHELXE | model building |
| SOLVE | phasing |
| RESOLVE | phasing |
| ARP/wARP | model building |
| CCP4 | phasing |
| O | model building |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2011-08-31 Deposition Author(s): Cuff, M.E., Li, H., Hatzos-Skintges, C., Tesar, C., Bearden, J., Clancy, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2011-08-31
Type: Initial release - Version 1.1: 2017-11-08
Changes: Refinement description - Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary
