4NG3

Crystal structure of 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis complexed with 4-Hydroxy-3-methoxy-5-nitrobenzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

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 from Sphingomonas paucimobilis complexed with 4-Hydroxy-3-methoxy-5-nitrobenzoic 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
1DF
Query on 1DF

Download Ideal Coordinates CCD File 
BA [auth F]
EA [auth G]
HA [auth H]
J [auth A]
M [auth B]
BA [auth F],
EA [auth G],
HA [auth H],
J [auth A],
M [auth B],
P [auth C],
S [auth D],
V [auth E]
4-hydroxy-3-methoxy-5-nitrobenzoic acid
C8 H7 N O6
AEDVAGWYAKIOIM-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
CA [auth F],
IA [auth H],
N [auth B],
W [auth E],
X [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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FA [auth G]
JA [auth H]
K [auth A]
KA [auth H]
Q [auth C]
FA [auth G],
JA [auth H],
K [auth A],
KA [auth H],
Q [auth C],
T [auth D],
Y [auth E],
Z [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth F]
DA [auth G]
GA [auth H]
I [auth A]
L [auth B]
AA [auth F],
DA [auth G],
GA [auth H],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.544α = 66.64
b = 100.399β = 67.96
c = 100.024γ = 88.24
Software Package:
Software NamePurpose
CBASSdata collection
BALBESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description