Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 135939.80 
• Atom Count: 9991 
• Residue Count: 1206 
• Unique protein chains: 1

4KGD

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

• DOI: 10.2210/pdb4KGD/pdb

• Classification: OXIDOREDUCTASE
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2013-04-29 Released: 2013-06-12 
• Deposition Author(s): Neumann, P., Tittmann, K.

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Experimental Data Snapshot

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

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

• PubMed: 23748673 
• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Pyruvate oxidase	A, B	603	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
PO4	A, B	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
TDP	A, B	THIAMIN DIPHOSPHATE C12 H18 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-N
FAD	A, B	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 119.280	α = 90.00
b = 154.160	β = 90.00
c = 165.470	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
SHELXL	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
ADSC	data collection
SHELX	refinement
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-29 
• Released Date: 2013-06-12 
• Deposition Author(s): Neumann, P., Tittmann, K.

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