7AN5

Enzyme of biosynthetic pathway

PDB DOI: https://doi.org/10.2210/pdb7AN5/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces coelicolor A3(2)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-10-11 Released: 2022-04-20
Deposition Author(s): Archna, A., Breithaupt, C., Stubbs, M.T.
Funding Organization(s): European Regional Development Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.236
R-Value Work: 0.202
R-Value Observed: 0.203

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Mechanism of chorismate dehydratase MqnA, the first enzyme of the futalosine pathway, proceeds via substrate-assisted catalysis

Prasad, A., Breithaupt, C., Nguyen, D.A., Lilie, H., Ziegler, J., Stubbs, M.T.

(2022) J Biol Chem : 102601

DOI: https://doi.org/10.1016/j.jbc.2022.102601

Macromolecule Content

Total Structure Weight: 65.54 kDa
Atom Count: 4,851
Modelled Residue Count: 565
Deposited Residue Count: 582
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chorismate dehydratase	A, B	291	Streptomyces coelicolor A3(2)	Mutation(s): 0 Gene Names: mqnA, SCO4506 EC: 4.2.1.151
UniProt
Find proteins for Q9L0T8 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9L0T8 Go to UniProtKB: Q9L0T8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9L0T8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RDH (Subject of Investigation/LOI) Query on RDH 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]	3-[(1-Carboxyvinyl)oxy]benzoic acid C₁₀ H₈ O₅ HGVAHYJMDVROLE-UHFFFAOYSA-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: 1.91 Å
R-Value Free: 0.236
R-Value Work: 0.202
R-Value Observed: 0.203
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.918	α = 90
b = 94.464	β = 95.2
c = 71.692	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-04-20

Deposition Author(s):

Funding Organization	Location	Grant Number
European Regional Development Fund	Germany	--

Revision History (Full details and data files)

Version 1.0: 2022-04-20
Type: Initial release
Version 1.1: 2022-04-27
Changes: Database references
Version 1.2: 2022-10-26
Changes: Database references
Version 1.3: 2024-01-31
Changes: Data collection, 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.