Download MendeleyThe Crystal Structure of Benzoylformate Decarboxylase from Polynucleobacter necessarius
Brodkin, H.R., Andrews, F.H., Novak, W.R.P., Petsko, G.A., Ringe, D., McLeish, M.J.To be published.
4K9Q
The Crystal Structure of Benzoylformate Decarboxylase from Polynucleobacter necessarius
- PDB DOI: https://doi.org/10.2210/pdb4K9Q/pdb
- Classification: LYASE
- Organism(s): Polynucleobacter necessarius
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2013-04-20 Released: 2014-04-23
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.189
- R-Value Work: 0.162
- R-Value Observed: 0.163
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 |
| Benzoylformate Decarboxylase | 539 | Polynucleobacter necessarius | Mutation(s): 0 Gene Names: Pnuc_1088 EC: 4.1.1.7 |  | |
UniProt | |||||
Find proteins for A4SXU0 (Polynucleobacter asymbioticus (strain DSM 18221 / CIP 109841 / QLW-P1DMWA-1)) Explore A4SXU0 Go to UniProtKB: A4SXU0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A4SXU0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TPP Query on TPP | D [auth A], F [auth B] | THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O |  | ||
| MG Query on MG | C [auth A], E [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.189
- R-Value Work: 0.162
- R-Value Observed: 0.163
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 67.737 | α = 90 |
| b = 104.953 | β = 90 |
| c = 158.731 | γ = 90 |
| Software Name | Purpose |
|---|---|
| BlueIce-Epics | data collection |
| PHENIX | model building |
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHENIX | phasing |
Entry History
Deposition Data
- Released Date: 2014-04-23 Deposition Author(s): Brodkin, H.R., Novak, W.R.P., McLeish, M.J.
Revision History (Full details and data files)
- Version 1.0: 2014-04-23
Type: Initial release - Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
