Download MendeleyStructure of acryloyl-CoA lyase PrpE from Dinoroseobacter shibae DFL 12
Zhang, Y.Z., Wang, P., Cao, H.Y.To be published.
5GXD
Structure of acryloyl-CoA lyase PrpE from Dinoroseobacter shibae DFL 12
- PDB DOI: 10.2210/pdb5GXD/pdb
- Classification: LYASE
- Organism(s): Dinoroseobacter shibae DFL 12 = DSM 16493
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-09-17 Released: 2017-09-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.194
- R-Value Work: 0.166
- R-Value Observed: 0.167
This is version 1.0 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 |
| AMP-dependent synthetase and ligase | A | 630 | Dinoroseobacter shibae DFL 12 = DSM 16493 | Mutation(s): 0 Gene Names: Dshi_0825 EC: 6.2.1 |  |
UniProt | |||||
Find proteins for A8LRC0 (Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12)) Explore A8LRC0 Go to UniProtKB: A8LRC0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A8LRC0 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| COA Query on COA | D [auth A] | COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N |  | Ligand Interaction | |
| AMP Query on AMP | B [auth A] | ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N |  | Ligand Interaction | |
| GOL Query on GOL | E [auth A], F [auth A], G [auth A], H [auth A], I [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| AKR Query on AKR | C [auth A] | ACRYLIC ACID C3 H4 O2 NIXOWILDQLNWCW-UHFFFAOYSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.194
- R-Value Work: 0.166
- R-Value Observed: 0.167
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 147.097 | α = 90 |
| b = 58.425 | β = 128.45 |
| c = 113.259 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-09-20 Deposition Author(s): Zhang, Y.Z., Wang, P., Cao, H.Y.
| Funding Organization | Location | Grant Number |
|---|---|---|
| China | -- |
Revision History (Full details and data files)
- Version 1.0: 2017-09-20
Type: Initial release
