4NI8

Crystal structure of 5-carboxyvanillate decarboxylase LigW from Sphingomonas paucimobilis complexed with Mn and 5-methoxyisophtalic acid

• PDB DOI: https://doi.org/10.2210/pdb4NI8/pdb

• Classification: LYASE
• Organism(s): Sphingomonas paucimobilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-05 Released: 2014-11-26 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Vladimirova, A., Raushel, F.M., Almo, S.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.175 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 

Starting Model: experimental

Literature

Crystal structure of 5-carboxyvanillate decarboxylase LigW from Sphingomonas paucimobilis complexed with Mn and 5-methoxyisophtalic acid

Fedorov, A.A., Fedorov, E.V., Vladimirova, A., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 299.88 kDa 
• Atom Count: 23,932 
• Modelled Residue Count: 2,680 
• Deposited Residue Count: 2,680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-carboxyvanillate decarboxylase	A, B, C, D, E, F, G, H	335	Sphingomonas paucimobilis	Mutation(s): 0  Gene Names: ligW
UniProt
Find proteins for Q8RJ47 (Sphingomonas paucimobilis) Explore Q8RJ47  Go to UniProtKB:  Q8RJ47

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1WB	AA [auth E], DA [auth F], J [auth A], KA [auth G], P [auth B], PA [auth H], S [auth C], X [auth D]	5-methoxybenzene-1,3-dicarboxylic acid C9 H8 O5 POSMIIJADZKUPL-UHFFFAOYSA-N
GOL	BA [auth E], EA [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	FA [auth F], GA [auth F], HA [auth F], IA [auth F], K [auth A], L [auth A], LA [auth G], M [auth A], MA [auth G], N [auth A], NA [auth G], Q [auth B], QA [auth H], RA [auth H], T [auth C], U [auth C], V [auth C], Y [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	CA [auth F], I [auth A], JA [auth G], O [auth B], OA [auth H], R [auth C], W [auth D], Z [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.175 
• R-Value Work: 0.148 
• R-Value Observed: 0.150 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.523	α = 67.04
b = 99.896	β = 88.44
c = 100.427	γ = 68.07

Software Package:

Software Name	Purpose
CBASS	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Vladimirova, A., Raushel, F.M., Almo, S.C.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description