4QTG

CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 COMPLEXED WITH MANGANESE

• PDB DOI: https://doi.org/10.2210/pdb4QTG/pdb

• Classification: HYDROLASE
• Organism(s): Novosphingobium aromaticivorans DSM 12444
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-07 Released: 2014-08-20 
• Deposition Author(s): Patskovsky, Y., Vladimirova, A., Toro, R., Bhosle, R., Gerlt, J.A., Raushel, F.M., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.164 
• R-Value Work: 0.120 
• R-Value Observed: 0.122 

Literature

Crystal Structure of 5-Carboxyvanillate Decarboxylase LIGW2 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: 85.39 kDa 
• Atom Count: 6,440 
• Modelled Residue Count: 697 
• Deposited Residue Count: 746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-CARBOXYVANILLATE DECARBOXYLASE	A, B	373	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	C [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.164 
• R-Value Work: 0.120 
• R-Value Observed: 0.122 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.468	α = 90
b = 85.486	β = 90
c = 141.623	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: 2014-08-20 
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: 2014-08-20
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description