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), 0.170 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.170 (DCC)
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

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

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.