4KGD | pdb_00004kgd

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

• PDB DOI: https://doi.org/10.2210/pdb4KGD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lactiplantibacillus plantarum JDM1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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 (Depositor), 0.143 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.125 (DCC) 
• R-Value Observed: 
  0.127 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1038/nchembio.1275
• Primary Citation Related Structures: 
  4KGD


• 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.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 135.94 kDa 
• Atom Count: 11,890 
• Modeled Residue Count: 1,171 
• Deposited Residue Count: 1,206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate oxidase	A, B	603	Lactiplantibacillus plantarum JDM1	Mutation(s): 0  Gene Names: JDM1_2870, pox5 EC: 1.2.3.3

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], L [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
TPP	F [auth A], N [auth B]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
PO4	E [auth A], O [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	G [auth A], H [auth A], I [auth A], J [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	K [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	D [auth A], M [auth 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 (Depositor), 0.143 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.125 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.28	α = 90
b = 154.16	β = 90
c = 165.47	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2013-08-07
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2021-08-04
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description