6TY7

Crystal structure of haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers

Markova, K.Kunka, A.Chmelova, K.Havlasek, M.Babkova, P.Marques, S.M.Vasina, M.Planas-Iglesias, J.Chaloupkova, R.Bednar, D.Prokop, Z.Damborsky, J.Marek, M.

(2021) ACS Catal 11: 12864-12885


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-1A, B299synthetic constructMutation(s): 0 
EC: 3.8.1.5
UniProt
Find proteins for P0A3G2 (Rhodococcus rhodochrous)
Explore P0A3G2 
Go to UniProtKB:  P0A3G2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3G2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES (Subject of Investigation/LOI)
Query on MES

Download Ideal Coordinates CCD File 
E [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
PG4 (Subject of Investigation/LOI)
Query on PG4

Download Ideal Coordinates CCD File 
G [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
F [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B],
J [auth B],
K [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NO3 (Subject of Investigation/LOI)
Query on NO3

Download Ideal Coordinates CCD File 
H [auth B]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.93α = 90
b = 75.65β = 90
c = 143.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionCzech RepublicMSCA-IF-2017 792772

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Advisory, Database references