6Y1C

X-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant D54F


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

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
R-specific alcohol dehydrogenase
A, B
262Levilactobacillus brevisMutation(s): 1 
Gene Names: radh
UniProt
Find proteins for Q84EX5 (Levilactobacillus brevis)
Explore Q84EX5 
Go to UniProtKB:  Q84EX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84EX5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
D [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

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N [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

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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

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E [auth A]
F [auth A]
L [auth B]
M [auth B]
O [auth B]
E [auth A],
F [auth A],
L [auth B],
M [auth B],
O [auth B],
P [auth B],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

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H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
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 = 55.76α = 90
b = 81.09β = 90
c = 113.13γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyWE2715/14-1

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