7TM6

Crystal structure of shikimate-3-phosphate and glyphosate bound 3-phosphoshikimate 1-carboxyvinyltransferase from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb7TM6/pdb

• Classification: TRANSFERASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae HS11286
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-01-19 Released: 2022-02-02 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.155 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 

Starting Model: experimental

Literature

Crystal structure of shikimate-3-phosphate and glyphosate bound 3-phosphoshikimate 1-carboxyvinyltransferase from Klebsiella pneumoniae

Liu, L., Lovell, S., Battaile, K.P., Tillery, L., Shek, R., Craig, J.K., Barrett, L.K., Van Voorhis, W.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 95.79 kDa 
• Atom Count: 7,926 
• Modelled Residue Count: 853 
• Deposited Residue Count: 870 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-phosphoshikimate 1-carboxyvinyltransferase	A, B	435	Klebsiella pneumoniae subsp. pneumoniae HS11286	Mutation(s): 0  Gene Names: aroA, KPHS_18160 EC: 2.5.1.19
UniProt
Find proteins for A0A0H3GV01 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GV01  Go to UniProtKB:  A0A0H3GV01

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S3P (Subject of Investigation/LOI)	C [auth A], F [auth B]	SHIKIMATE-3-PHOSPHATE C7 H11 O8 P QYOJSKGCWNAKGW-PBXRRBTRSA-N
1PE	E [auth A], H [auth B], I [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
GPJ (Subject of Investigation/LOI)	D [auth A], G [auth B]	GLYPHOSATE C3 H9 N O5 P XDDAORKBJWWYJS-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
S3P	BindingDB:  7TM6	Kd: min: 7000, max: 8000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.155 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M37TM6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.243	α = 90
b = 115.22	β = 90
c = 183.266	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description