6Y10 | pdb_00006y10

X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant Q126H

• PDB DOI: https://doi.org/10.2210/pdb6Y10/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Levilactobacillus brevis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-02-10 Released: 2020-02-19 
• Deposition Author(s): Hermann, J., Bischoff, D., Janowski, R., Niessing, D., Grob, P., Hekmat, D., Weuster-Botz, D.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 
  0.164 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Controlling 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

• DOI: https://doi.org/10.3390/cryst11060588

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 28.48 kDa 
• Atom Count: 2,520 
• Modeled Residue Count: 251 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
R-specific alcohol dehydrogenase	A	262	Levilactobacillus brevis	Mutation(s): 1  Gene Names: radh
UniProt
Find proteins for Q84EX5 (Levilactobacillus brevis) Explore Q84EX5  Go to UniProtKB:  Q84EX5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A], K [auth A], L [auth A], M [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free:  0.164 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.05	α = 90
b = 80.57	β = 90
c = 113.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	WE2715/14-1

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 2.0: 2020-09-30
  Type: Coordinate replacement
  Reason: Atomic clashes
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2021-06-09
  Changes: Database references
• Version 2.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description