Download MendeleyThe structure of a restriction endonuclease-like fold superfamily protein from Spirosoma linguale.
Cuff, M.E., Tesar, C., Samano, S., Bearden, J., Joachimiak, A.To be published.
3IJM
The structure of a restriction endonuclease-like fold superfamily protein from Spirosoma linguale.
- PDB DOI: https://doi.org/10.2210/pdb3IJM/pdb
- Classification: structural genomics, unknown function
- Organism(s): Spirosoma linguale DSM 74
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2009-08-04 Released: 2009-09-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.199
- R-Value Work: 0.166
- R-Value Observed: 0.168
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 |
| uncharacterized restriction endonuclease-like fold superfamily protein | 151 | Spirosoma linguale DSM 74 | Mutation(s): 0 Gene Names: DUF820, SlinDRAFT_22400 |  | |
UniProt | |||||
Find proteins for D2QNN3 (Spirosoma linguale (strain ATCC 33905 / DSM 74 / LMG 10896 / Claus 1)) Explore D2QNN3 Go to UniProtKB: D2QNN3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D2QNN3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | D [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | C [auth A], F [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| NA Query on NA | E [auth A] | SODIUM ION Na FKNQFGJONOIPTF-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: 1.70 Å
- R-Value Free: 0.199
- R-Value Work: 0.166
- R-Value Observed: 0.168
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 65.77 | α = 90 |
| b = 65.849 | β = 90 |
| c = 68.917 | 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: 2009-09-22 Deposition Author(s): Cuff, M.E., Tesar, C., Samano, S., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-09-22
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description
