Download MendeleyHigh Resolution Structure of Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate;
Bera, A.K., Anderson, N.L., Hasson, M.S.To be published.
1YNO
High Resolution Structure of Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate
- PDB DOI: https://doi.org/10.2210/pdb1YNO/pdb
- Classification: LYASE
- Organism(s): Pseudomonas putida
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2005-01-24 Released: 2006-01-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.22 Å
- R-Value Free: 0.155
- R-Value Work: 0.124
This is version 1.3 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 | 527 | Pseudomonas putida | Mutation(s): 0 Gene Names: mdlC EC: 4.1.1.7 |  | |
UniProt | |||||
Find proteins for P20906 (Pseudomonas putida) Explore P20906 Go to UniProtKB: P20906 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P20906 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TZD Query on TZD | F [auth A] | 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN
DIPHOSPHATE C12 H18 N4 O8 P2 S ZGJUYGIRPQSCFA-UHFFFAOYSA-N |  | ||
| CA Query on CA | C [auth A], D [auth A], E [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| MG Query on MG | B [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.22 Å
- R-Value Free: 0.155
- R-Value Work: 0.124
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 80.951 | α = 90 |
| b = 95.46 | β = 90 |
| c = 136.701 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | refinement |
| CNS | phasing |
| SHELXL-97 | refinement |
Entry History
Deposition Data
- Released Date: 2006-01-17 Deposition Author(s): Bera, A.K., Hasson, M.S.
Revision History (Full details and data files)
- Version 1.0: 2006-01-17
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Atomic model, Derived calculations, Version format compliance - Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description
