6F6T | pdb_00006f6t

Phenylalanine ammonia-lyase (PAL) from Petroselinum crispum complexed with S-APPA

• PDB DOI: https://doi.org/10.2210/pdb6F6T/pdb

• Classification: LYASE
• Organism(s): Petroselinum crispum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-12-06 Released: 2019-06-26 
• Deposition Author(s): Bata, Z., Leveles, I., Vertessy, G.B., Poppe, L.
• Funding Organization(s): National Research Development and Innovation Office, EU COST, Hungarian OTKA Foundation, Romanian Ministry for European Funds

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Substrate Tunnel Engineering Aided by X-ray Crystallography and Functional Dynamics Swaps the Function of MIO-Enzymes

Bata, Z., Molnar, Z., Madaras, E., Molnar, B., Santa-Bell, E., Varga, A., Leveles, I., Qian, R., Hammerschmidt, F., Paizs, C., Vertessy, B.G., Poppe, L.

(2021) ACS Catal : 4538-4549

• DOI: https://doi.org/10.1021/acscatal.1c00266

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: 156.12 kDa 
• Atom Count: 10,962 
• Modeled Residue Count: 1,352 
• Deposited Residue Count: 1,428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanine ammonia-lyase 1	A, B	714	Petroselinum crispum	Mutation(s): 3  Gene Names: PAL1 EC: 4.3.1.24
UniProt
Find proteins for P24481 (Petroselinum crispum) Explore P24481  Go to UniProtKB:  P24481

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CV2 (Subject of Investigation/LOI)	C [auth A], D [auth B]	(S)-(1-amino-2phenylallyl)phosphonic acid C9 H12 N O3 P JUVPNYIYKLIRHO-VIFPVBQESA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MDO	A, B	L-PEPTIDE LINKING	C8 H11 N3 O3		ALA, SER, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.74	α = 90
b = 161.1	β = 90
c = 141.65	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Bata, Z., Leveles, I., Vertessy, G.B., Poppe, L.

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Funding Organization	Location	Grant Number
National Research Development and Innovation Office	Hungary	NKFIH K119493
National Research Development and Innovation Office	Hungary	NKFIH K109486
National Research Development and Innovation Office	Hungary	NVKP-16-1-2016-0020
National Research Development and Innovation Office	Hungary	VEKOP-2.3.2-16-2017-00013
National Research Development and Innovation Office	Hungary	ICGEB CRP/HUN14-01
National Research Development and Innovation Office	Hungary	UNKP-2017-3-058
EU COST	Hungary	Action CM1303 SysBiocat
Hungarian OTKA Foundation	Hungary	NN-103242
Romanian Ministry for European Funds	Romania	NEMSyB ID P37273 Cod MySMIS 103413

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2021-04-07
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2021-04-14
  Changes: Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-01-17
  Changes: Refinement description
• Version 3.0: 2025-10-01
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary