7CX1

Crystal structure of a tyrosine decarboxylase from Enterococcus faecalis in complex with the cofactor PLP and inhibitor methyl-tyrosine

• PDB DOI: https://doi.org/10.2210/pdb7CX1/pdb

• Classification: LYASE
• Organism(s): Enterococcus faecalis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-09-01 Released: 2021-09-01 
• Deposition Author(s): Yu, X., Gong, M., Huang, J., Liu, W., Chen, C., Guo, R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a tyrosine decarboxylase from Enterococcus faecalis in complex with the cofactor PLP and inhibitor methyl-tyrosine

Yu, X., Gong, M., Huang, J., Liu, W., Chen, C., Guo, R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 211.75 kDa 
• Atom Count: 14,438 
• Modelled Residue Count: 1,795 
• Deposited Residue Count: 1,860 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decarboxylase	A, B, C	620	Enterococcus faecalis	Mutation(s): 0  Gene Names: tyrDC, ddc, ELS84_1624, KUB3007_C03520, NCTC8729_00604 EC: 4.1.1.86 (PDB Primary Data), 4.1.1.25 (UniProt), 4.1.1 (UniProt)
UniProt
Find proteins for Q838D6 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q838D6  Go to UniProtKB:  Q838D6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GKU (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth B], G [auth C]	4-[(2R)-2-(methylamino)propyl]phenol C10 H15 N O SBUQZKJEOOQSBV-MRVPVSSYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.49	α = 90
b = 131.49	β = 90
c = 385.66	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-01 
Deposition Author(s): Yu, X., Gong, M., Huang, J., Liu, W., Chen, C., Guo, R.

Revision History  

• Version 1.0: 2021-09-01
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description