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 

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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
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  • 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

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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