6WAO | pdb_00006wao

Crystal structure of Arabidopsis thaliana isochorismoyl-glutamate A pyruvoyl-glutamate lyase in complex with (2-(3-carboxyphenoxy)acetyl)-L-glutamic acid

PDB DOI: https://doi.org/10.2210/pdb6WAO/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-03-25 Released: 2021-08-04
Deposition Author(s): Torrens-Spence, M.P., Weng, J.K.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.212 (Depositor), 0.210 (DCC)
R-Value Work:
0.172 (Depositor)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The structural basis of the isochorismoyl-glutamate pyruvoyl-glutamate lyase activity of Arabidopsis EPS1 in salicylic acid biosynthesis

Torrens-Spence, M.P., Weng, J.K.

To be published.

Macromolecule Content

Total Structure Weight: 98.04 kDa
Atom Count: 7,426
Modeled Residue Count: 837
Deposited Residue Count: 868
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein ENHANCED PSEUDOMONAS SUSCEPTIBILITY 1	A, B	434	Arabidopsis thaliana	Mutation(s): 0 Gene Names: EPS1, At5g67160, K21H1.12 EC: 2.3.1
UniProt
Find proteins for Q9FH97 (Arabidopsis thaliana) Explore Q9FH97 Go to UniProtKB: Q9FH97
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9FH97
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TQG (Subject of Investigation/LOI) Query on TQG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	N-[(3-carboxyphenoxy)acetyl]-L-glutamic acid C₁₄ H₁₅ N O₈ ZYEJDCAIACBLPZ-JTQLQIEISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.212 (Depositor), 0.210 (DCC)
R-Value Work: 0.172 (Depositor)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.136	α = 90
b = 75.353	β = 90
c = 193.513	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
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: 2021-08-04

Deposition Author(s):

Torrens-Spence, M.P.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1709616

Revision History (Full details and data files)

Version 1.0: 2021-08-04
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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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.