Download MendeleyThe crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase protein from Planctomyces limnophilus dsm 3776
Wu, R., Bearden, J., Kim, Y., Joachimiak, A.To be published.
4RT5
The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase protein from planctomyces limnophilus dsm 3776
- PDB DOI: https://doi.org/10.2210/pdb4RT5/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Planctopirus limnophila DSM 3776
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2014-11-13 Released: 2014-12-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 ?
- R-Value Free: 0.180
- R-Value Work: 0.151
- R-Value Observed: 0.153
wwPDB Validation 3D Report Full Report
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 |
| Glyoxalase/bleomycin resistance protein/dioxygenase | 114 | Planctopirus limnophila DSM 3776 | Mutation(s): 0 Gene Names: Plim_1428 EC: 4.4.1.5 |  | |
UniProt | |||||
Find proteins for D5SVJ2 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SVJ2 Go to UniProtKB: D5SVJ2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D5SVJ2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TRS Query on TRS | D [auth A], E [auth A], G [auth B] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O |  | ||
| GOL Query on GOL | H [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| NI Query on NI | C [auth A], F [auth B] | 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: 1.50 ?
- R-Value Free: 0.180
- R-Value Work: 0.151
- R-Value Observed: 0.153
- Space Group: P 1 21 1
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 30.13 | ¦Á = 90 |
| b = 77.496 | ¦Â = 109.19 |
| c = 45.827 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| HKL-3000 | data collection |
| MLPHARE | phasing |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
Entry History
Deposition Data
- Released Date: 2014-12-03 Deposition Author(s): Wu, R., Bearden, J., Kim, Y., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2014-12-03
Type: Initial release - Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary
