6RGS | pdb_00006rgs

Crystal Structure of Phenylalanine Ammonia Lyase (PAL) from Petroselinum crispum bound to cinnamate

PDB DOI: https://doi.org/10.2210/pdb6RGS/pdb

Classification: LYASE
Organism(s): Petroselinum crispum
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2019-04-17 Released: 2019-09-04
Deposition Author(s): Brem, J., Lang, P., Bencze, C.-L., Schofield, C.
Funding Organization(s): Medical Research Council (United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.210 (Depositor), 0.212 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Mapping the Hydrophobic Substrate Binding Site of Phenylalanine Ammonia Lyase from Petroselinum crispum

Nagy, E.Z.A., Tork, S.D., Lang, P.A., Filip, A., Irimie, F.D., Poppe, L., Tosa, M.I., Schofield, C.J., Brem, J., Paizs, C., Bencze, L.C.

(2019) ACS Catal

DOI: https://doi.org/10.1021/acscatal.9b02108

Macromolecule Content

Total Structure Weight: 162.15 kDa
Atom Count: 9,415
Modeled Residue Count: 1,254
Deposited Residue Count: 1,480
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanine ammonia-lyase 1	A, B	740	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24481
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K3Z Query on K3Z Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	(E)-3-(4-methoxyphenyl)acrylic acid C₁₀ H₁₀ O₃ AFDXODALSZRGIH-QPJJXVBHSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.210 (Depositor), 0.212 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.91	α = 90
b = 159.82	β = 90
c = 142.72	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2019-09-04
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2024-01-24
Changes: Refinement description
Version 2.2: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.