4KGD

High-resolution crystal structure of pyruvate oxidase from L. plantarum in complex with phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Observation of a stable carbene at the active site of a thiamin enzyme.

Meyer, D.Neumann, P.Ficner, R.Tittmann, K.

(2013) Nat.Chem.Biol. 9: 488-490

  • DOI: 10.1038/nchembio.1275

  • PubMed Abstract: 
  • Carbenes are highly reactive chemical compounds that are exploited as ligands in organometallic chemistry and are powerful organic catalysts. They were postulated to occur as transient intermediates in enzymes, yet their existence in a biological sys ...

    Carbenes are highly reactive chemical compounds that are exploited as ligands in organometallic chemistry and are powerful organic catalysts. They were postulated to occur as transient intermediates in enzymes, yet their existence in a biological system could never be demonstrated directly. We present spectroscopic and structural data of a thiamin enzyme in a noncovalent complex with substrate, which implicate accumulation of a stable carbene as a major resonance contributor to deprotonated thiamin.


    Organizational Affiliation

    Albrecht-von-Haller Institute, Göttingen Center for Molecular Biosciences, Ernst-Caspari-Haus, Georg-August University Göttingen, Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate oxidase
A, B
603N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
TDP
Query on TDP

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A, B
THIAMIN DIPHOSPHATE
C12 H18 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.127 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 119.280α = 90.00
b = 154.160β = 90.00
c = 165.470γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SHELXLrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
ADSCdata collection
SHELXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Database references
  • Version 1.2: 2013-08-07
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description