6MLS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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

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

(2020) ACS Catal 10: 1692-1703


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine phenol-lyase456Citrobacter freundiiMutation(s): 0 
Gene Names: tpl
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine phenol-lyase456Citrobacter freundiiMutation(s): 0 
Gene Names: tpl
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33

Download Ideal Coordinates CCD File 
I [auth B]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
0JO
Query on 0JO

Download Ideal Coordinates CCD File 
F [auth A]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
Query on CQG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth A]
pyridin-4-ol
C5 H5 N O
GCNTZFIIOFTKIY-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A],
G [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.64α = 90
b = 133.51β = 90
c = 143.08γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2020-04-15
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.3: 2023-11-15
    Changes: Data collection