4QRN

HIGH-RESOLUTION CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 COMPLEXED WITH MANGANESE AND 4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of 5-Carboxyvanillate Decarboxylase from Novosphingobium Aromaticivorans

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5-Carboxyvanillate Decarboxylase
A, B, C, D
373Novosphingobium aromaticivorans DSM 12444Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2GA79
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1DF
Query on 1DF

Download Ideal Coordinates CCD File 
F [auth A],
N [auth B],
R [auth C],
X [auth D]
4-hydroxy-3-methoxy-5-nitrobenzoic acid
C8 H7 N O6
AEDVAGWYAKIOIM-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
O [auth B]
S [auth C]
T [auth C]
G [auth A],
H [auth A],
O [auth B],
S [auth C],
T [auth C],
Y [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
L [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
M [auth B],
Q [auth C],
W [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth D]
I [auth A]
J [auth A]
K [auth A]
P [auth B]
AA [auth D],
I [auth A],
J [auth A],
K [auth A],
P [auth B],
U [auth C],
V [auth C],
Z [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.136 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.723α = 90
b = 60.747β = 103.33
c = 130.517γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data 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: 2014-08-06
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description