4L6D

Crystal structure of 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis complexed with vanillic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

Starting Model: experimental
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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 Sphingomonas paucimobilis complexed with vanillic 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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
BA [auth D]
GA [auth E]
LA [auth F]
M [auth A]
QA [auth G]
BA [auth D],
GA [auth E],
LA [auth F],
M [auth A],
QA [auth G],
S [auth B],
UA [auth H],
W [auth C]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
VNL
Query on VNL

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AA [auth D]
DA [auth E]
EA [auth E]
FA [auth E]
J [auth A]
AA [auth D],
DA [auth E],
EA [auth E],
FA [auth E],
J [auth A],
JA [auth F],
K [auth A],
KA [auth F],
L [auth A],
NA [auth G],
OA [auth G],
P [auth B],
PA [auth G],
Q [auth B],
R [auth B],
SA [auth H],
TA [auth H],
U [auth C],
V [auth C],
Z [auth D]
4-HYDROXY-3-METHOXYBENZOATE
C8 H7 O4
WKOLLVMJNQIZCI-UHFFFAOYSA-M
PEG
Query on PEG

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HA [auth E]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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X [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN
Query on MN

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CA [auth E]
I [auth A]
IA [auth F]
MA [auth G]
N [auth A]
CA [auth E],
I [auth A],
IA [auth F],
MA [auth G],
N [auth A],
O [auth B],
RA [auth H],
T [auth C],
Y [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.592α = 109.71
b = 96.917β = 90.53
c = 97.029γ = 111.89
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