4K9Q

The Crystal Structure of Benzoylformate Decarboxylase from Polynucleobacter necessarius


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

The Crystal Structure of Benzoylformate Decarboxylase from Polynucleobacter necessarius

Brodkin, H.R.Andrews, F.H.Novak, W.R.P.Petsko, G.A.Ringe, D.McLeish, M.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Benzoylformate DecarboxylaseA, B539Polynucleobacter necessariusMutation(s): 0 
Gene Names: Pnuc_1088
EC: 4.1.1.7
UniProt
Find proteins for A4SXU0 (Polynucleobacter asymbioticus (strain DSM 18221 / CIP 109841 / QLW-P1DMWA-1))
Explore A4SXU0 
Go to UniProtKB:  A4SXU0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP (Subject of Investigation/LOI)
Query on TPP

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.737α = 90
b = 104.953β = 90
c = 158.731γ = 90
Software Package:
Software NamePurpose
BlueIce-Epicsdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release