4NI8

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


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
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-carboxyvanillate decarboxylase
A, B, C, D, E
A, B, C, D, E, F, G, H
335Sphingomonas paucimobilisMutation(s): 0 
Gene Names: ligW
UniProt
Find proteins for Q8RJ47 (Sphingomonas paucimobilis)
Explore Q8RJ47 
Go to UniProtKB:  Q8RJ47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RJ47
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1WB
Query on 1WB

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth F]
J [auth A]
KA [auth G]
P [auth B]
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
Query on GOL

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BA [auth E],
EA [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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FA [auth F]
GA [auth F]
HA [auth F]
IA [auth F]
K [auth A]
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
Query on MN

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CA [auth F]
I [auth A]
JA [auth G]
O [auth B]
OA [auth H]
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 = 80.523α = 67.04
b = 99.896β = 88.44
c = 100.427γ = 68.07
Software Package:
Software NamePurpose
CBASSdata collection
BALBESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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