6MME

Citrobacter freundii tyrosine phenol-lyase complexed with 4-hydroxypyridine and aminoacrylate from S-ethyl-L-cysteine

• PDB DOI: https://doi.org/10.2210/pdb6MME/pdb

• Classification: LYASE
• Organism(s): Citrobacter freundii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-09-30 Released: 2019-10-02 
• Deposition Author(s): Phillips, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.198 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 

Starting Model: experimental

Literature

Pressure and Temperature Effects on the Formation of Aminoacrylate Intermediates of Tyrosine Phenol-lyase Demonstrate Reaction Dynamics

Phillips, R.S., Crasi, S., Kovalevsky, A., Gerlits, O., Weiss, K., Iorgu, A.I., Heyes, D.J., Hay, S.

(2020) ACS Catal 10: 1692-1703

• DOI: https://doi.org/10.1021/acscatal.9b03967

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 104.46 kDa 
• Atom Count: 8,778 
• Modelled Residue Count: 910 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine phenol-lyase	A, B	456	Citrobacter freundii	Mutation(s): 0  Gene Names: tpl EC: 4.1.99.2
UniProt
Find proteins for P31013 (Citrobacter freundii) Explore P31013  Go to UniProtKB:  P31013

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	I [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
0JO	F [auth A], J [auth B]	2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid C11 H13 N2 O7 P BHIGINKEEFZJGX-YIXHJXPBSA-N
CQG	D [auth A], E [auth A], H [auth A]	pyridin-4-ol C5 H5 N O GCNTZFIIOFTKIY-UHFFFAOYSA-N
K	C [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.198 
• R-Value Work: 0.164 
• R-Value Observed: 0.164 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.72	α = 90
b = 133.3	β = 90
c = 144.19	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-02 
Deposition Author(s): Phillips, R.S.

Revision History  

• Version 1.0: 2019-10-02
  Type: Initial release
  
• Version 1.1: 2020-10-14
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description