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 

wwPDB Validation 3D Report Full Report



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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5-carboxyvanillate decarboxylaseABCDEFGH335Sphingomonas paucimobilisMutation(s): 0 
Gene Names: ligW
Find proteins for Q8RJ47 (Sphingomonas paucimobilis)
Explore Q8RJ47 
Go to UniProtKB:  Q8RJ47
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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A, B, C, D, E, F, G, H
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
VNL
Query on VNL

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A, B, C, D, E, F, G, H
4-HYDROXY-3-METHOXYBENZOATE
C8 H7 O4
WKOLLVMJNQIZCI-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

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E
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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A, B, C, D, E, F, G, H
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
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



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-13
    Type: Initial release