1QXO | pdb_00001qxo

Crystal structure of Chorismate synthase complexed with oxidized FMN and EPSP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.222 (Depositor) 
  • R-Value Work: 
    0.157 (Depositor) 
  • R-Value Observed: 
    0.160 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

The structure of chorismate synthase reveals a novel flavin binding site fundamental to a unique chemical reaction

Maclean, J., Ali, S.

(2003) Structure 11: 1499-1511

  • DOI: https://doi.org/10.1016/j.str.2003.11.005
  • Primary Citation Related Structures: 
    1QXO

  • PubMed Abstract: 

    The crystal structure of chorismate synthase (CS) from Streptococcus pneumoniae has been solved to 2.0 A resolution in the presence of flavin mononucleotide (FMN) and the substrate 5-enolpyruvyl-3-shikimate phosphate (EPSP). CS catalyses the final step of the shikimate pathway and is a potential therapeutic target for the rational design of novel antibacterials, antifungals, antiprotozoals, and herbicides. CS is a tetramer with the monomer possessing a novel beta-alpha-beta fold. The interactions between the enzyme, cofactor, and substrate reveal the structural reasons underlying the unique catalytic mechanism and identify the amino acids involved. This structure provides the essential initial information necessary for the generation of novel anti-infective compounds by a structure-guided medicinal chemistry approach.

    • Organizational Affiliation: 
    • Department of Structural Biology, West of Scotland Science Park, Glasgow G20 0XP, Scotland, United Kingdom. john.maclean@btinternet.com

Macromolecule Content 

  • Total Structure Weight: 179.9 kDa 
  • Atom Count: 14,427 
  • Modeled Residue Count: 1,552 
  • Deposited Residue Count: 1,552 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chorismate synthase
A, B, C, D
388Streptococcus pneumoniaeMutation(s): 12 
Gene Names: AROC, SP1374 OR SPR1232
EC: 4.2.3.5
UniProt
Find proteins for P0A2Y6 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P0A2Y6 
Go to UniProtKB:  P0A2Y6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A2Y6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN

Query on FMN


Download:Ideal Coordinates CCD File
BA [auth D]
CA [auth D]
K [auth A]
P [auth B]
U [auth C]
BA [auth D],
CA [auth D],
K [auth A],
P [auth B],
U [auth C],
V [auth C]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
EPS

Query on EPS


Download:Ideal Coordinates CCD File
DA [auth D],
L [auth A],
Q [auth B],
W [auth C]		5-[(1-CARBOXYVINYL)OXY]-4-HYDROXY-3-(PHOSPHONOOXY)CYCLOHEX-1-ENE-1-CARBOXYLIC ACID
C10 H13 O10 P
QUTYKIXIUDQOLK-PRJMDXOYSA-N
NCO

Query on NCO


Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
M [auth B]
N [auth B]
E [auth A],
F [auth A],
G [auth A],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
X [auth D],
Y [auth D]
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
AA [auth D]
H [auth A]
I [auth A]
J [auth A]
O [auth B]
AA [auth D],
H [auth A],
I [auth A],
J [auth A],
O [auth B],
T [auth C],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.222 (Depositor) 
  • R-Value Work:  0.157 (Depositor) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.059α = 90
b = 124.582β = 115.15
c = 85.163γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
REFMACrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary