4QS6

CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 (TARGET EFI-505250) WITH BOUND 4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID, NO METAL, THE D314N MUTANT

• PDB DOI: https://doi.org/10.2210/pdb4QS6/pdb

• Classification: HYDROLASE
• Organism(s): Novosphingobium aromaticivorans DSM 12444
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-07-03 Released: 2014-08-06 
• Deposition Author(s): Patskovsky, Y., Vladimirova, A., Toro, R., Bhosle, R., Gerlt, J.A., Raushel, F.M., Almo, S.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.205 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Ligw2 Decarboxylase from Novosphingobium Aromaticivorans

Patskovsky, Y., Vladimirova, A., Toro, R., Bhosle, R., Raushel, F.M., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 85.68 kDa 
• Atom Count: 6,435 
• Modelled Residue Count: 698 
• Deposited Residue Count: 746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ligw2 Decarboxylase	A, B	373	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 1  Gene Names: Saro_0799
UniProt
Find proteins for Q2GA79 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore Q2GA79  Go to UniProtKB:  Q2GA79

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1DF	F [auth A], I [auth B]	4-hydroxy-3-methoxy-5-nitrobenzoic acid C8 H7 N O6 AEDVAGWYAKIOIM-UHFFFAOYSA-N
GOL	C [auth A], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.205 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.422	α = 90
b = 85.396	β = 90
c = 141.616	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-06 
Deposition Author(s): Patskovsky, Y., Vladimirova, A., Toro, R., Bhosle, R., Gerlt, J.A., Raushel, F.M., Almo, S.C.

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description