2YHK

D214A mutant of tyrosine phenol-lyase from Citrobacter freundii

• PDB DOI: https://doi.org/10.2210/pdb2YHK/pdb

• Classification: LYASE
• Organism(s): Citrobacter freundii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-05-03 Released: 2012-05-02 
• Deposition Author(s): Milic, D., Demidkina, T.V., Matkovic-Calogovic, D., Antson, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.177 
• R-Value Work: 0.156 
• R-Value Observed: 0.156 

Starting Model: experimental

Literature

Crystal Structure of Citrobacter Freundii Asp214Ala Tyrosine Phenol-Lyase Reveals that Asp214 is Critical for Maintaining a Strain in the Internal Aldimine

Milic, D., Demidkina, T.V., Zakomirdina, L.N., Matkovic-Calogovic, D., Antson, A.A.

(2012) Croat Chem Acta 85: 283

• DOI: https://doi.org/10.5562/CCA1915

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: 104.78 kDa 
• Atom Count: 8,157 
• 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): 1  EC: 4.1.99.2
UniProt
Find proteins for P31013 (Citrobacter freundii) Explore P31013  Go to UniProtKB:  P31013

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	K [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
PLP	I [auth A], N [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
K	C [auth A], J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.177 
• R-Value Work: 0.156 
• R-Value Observed: 0.156 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.605	α = 90
b = 142.705	β = 90
c = 59.412	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Milic, D., Demidkina, T.V., Matkovic-Calogovic, D., Antson, A.A.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2012-11-28
  Changes: Database references
• Version 1.2: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary