7CX0 | pdb_00007cx0

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

• PDB DOI: https://doi.org/10.2210/pdb7CX0/pdb

• Classification: LYASE
• Organism(s): Enterococcus faecalis
• Expression System: Escherichia coli BL21(DE3)
• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.268 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

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

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: 211.82 kDa 
• Atom Count: 14,216 
• Modeled Residue Count: 1,793 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	D [auth A], F [auth B], H [auth C]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
142 (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C]	CARBIDOPA C10 H14 N2 O4 TZFNLOMSOLWIDK-JTQLQIEISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.268 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.696	α = 90
b = 131.696	β = 90
c = 390.014	γ = 120

Software Package:

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