Download MendeleyControlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts
Hermann, J., Bischoff, D., Grob, P., Janowski, R., Hekmat, D., Niessing, D., Zacharias, M., Weuster-Botz, D.(2021) Crystals (Basel) 11
6Y1C
X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant D54F
- PDB DOI: https://doi.org/10.2210/pdb6Y1C/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Levilactobacillus brevis
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2020-02-11 Released: 2020-02-19
- Funding Organization(s): German Research Foundation (DFG)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.41 Å
- R-Value Free: 0.162
- R-Value Work: 0.126
- R-Value Observed: 0.127
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 2.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| R-specific alcohol dehydrogenase | 262 | Levilactobacillus brevis | Mutation(s): 1 Gene Names: radh |  | |
UniProt | |||||
Find proteins for Q84EX5 (Levilactobacillus brevis) Explore Q84EX5 Go to UniProtKB: Q84EX5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q84EX5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PG4 Query on PG4 | D [auth A] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| PGE Query on PGE | N [auth B] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | C [auth A], I [auth B], J [auth B], K [auth B] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | E [auth A] F [auth A] L [auth B] M [auth B] O [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CL Query on CL | H [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | G [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.41 Å
- R-Value Free: 0.162
- R-Value Work: 0.126
- R-Value Observed: 0.127
- Space Group: P 21 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 55.76 | α = 90 |
| b = 81.09 | β = 90 |
| c = 113.13 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-02-19 Deposition Author(s): Hermann, J., Bischoff, D., Janowski, R., Niessing, D., Grob, P., Hekmat, D., Weuster-Botz, D.
| Funding Organization | Location | Grant Number |
|---|---|---|
| German Research Foundation (DFG) | Germany | WE2715/14-1 |
Revision History (Full details and data files)
- Version 1.0: 2020-02-19
Type: Initial release - Version 1.1: 2020-03-04
Changes: Derived calculations - Version 2.0: 2020-09-23
Type: Coordinate replacement
Reason: Atomic clashes
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2021-06-09
Changes: Database references - Version 2.2: 2024-01-24
Changes: Data collection, Database references, Refinement description
