Download MendeleyCrystal Structure of Putative Phytanoyl-CoA Dioxygenase Family Protein YbiU from Yersinia pestis
Kim, Y., Chhor, G., Endres, M., Babnigg, G., Joachimiak, A.To be published.
4RGK
Crystal Structure of Putative Phytanoyl-CoA Dioxygenase Family Protein YbiU from Yersinia pestis
- PDB DOI: https://doi.org/10.2210/pdb4RGK/pdb
- Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
- Organism(s): Yersinia pestis
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2014-09-30 Released: 2014-12-31
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.241
- R-Value Work: 0.191
- R-Value Observed: 0.194
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 |
| Uncharacterized protein | 418 | Yersinia pestis | Mutation(s): 0 Gene Names: y1506, YPO2976, YP_2601 |  | |
UniProt | |||||
Find proteins for A0A2U2H2N4 (Yersinia pestis) Explore A0A2U2H2N4 Go to UniProtKB: A0A2U2H2N4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A2U2H2N4 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | B [auth A], G [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | C [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | D [auth A], E [auth A], F [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.15 Å
- R-Value Free: 0.241
- R-Value Work: 0.191
- R-Value Observed: 0.194
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 115.75 | α = 90 |
| b = 54.659 | β = 124.47 |
| c = 93.152 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| HKL-3000 | data collection |
| HKL-3000 | phasing |
| SHELXCD | phasing |
| SHELXE | model building |
| MLPHARE | phasing |
| DM | model building |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| DM | phasing |
Entry History
Deposition Data
- Released Date: 2014-12-31 Deposition Author(s): Kim, Y., Chhor, G., Endres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2014-12-31
Type: Initial release - Version 1.1: 2017-11-22
Changes: Refinement description
