2YHK

D214A mutant of tyrosine phenol-lyase from Citrobacter freundii


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
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TYROSINE PHENOL-LYASE
A, B
456Citrobacter freundiiMutation(s): 1 
EC: 4.1.99.2
UniProt
Find proteins for P31013 (Citrobacter freundii)
Explore P31013 
Go to UniProtKB:  P31013
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31013
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33

Download Ideal Coordinates CCD File 
K [auth B]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
PLP
Query on PLP

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I [auth A],
N [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
D [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

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E [auth A]
F [auth A]
G [auth A]
H [auth A]
L [auth B]
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
Query on K

Download Ideal Coordinates CCD File 
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 = 132.605α = 90
b = 142.705β = 90
c = 59.412γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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