6G75 | pdb_00006g75

Crystal structure of the common ancestor of haloalkane dehalogenases and Renilla luciferase (AncHLD-RLuc)

• PDB DOI: https://doi.org/10.2210/pdb6G75/pdb

• Classification: HYDROLASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-04-04 Released: 2019-04-24 
• Deposition Author(s): Chaloupkova, R., Waterman, J., Marek, M., Damborsky, J.
• Funding Organization(s): Grant Agency of the Czech Republic

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.190 (Depositor), 0.151 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts

Chaloupkova, R., Liskova, V., Toul, M., Markova, K., Sebestova, E., Hernychova, L., Marek, M., Pinto, G.P., Pluskal, D., Waterman, J., Prokop, Z., Damborsky, J.

(2019) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.9b01031

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 68.63 kDa 
• Atom Count: 5,368 
• Modeled Residue Count: 592 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Common ancestor of haloalkane dehalogenase and Renilla luciferase (AncHLD-RLuc)	A, B	296	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth A], H [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD	D [auth A], G [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
OXY	C [auth A], F [auth B]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.190 (Depositor), 0.151 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.549	α = 90
b = 60.51	β = 90.9
c = 123.63	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Chaloupkova, R., Waterman, J., Marek, M., Damborsky, J.

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Funding Organization	Location	Grant Number
Grant Agency of the Czech Republic	Czech Republic	16-24223S

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2020-05-06
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description