7TM5

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

• PDB DOI: https://doi.org/10.2210/pdb7TM5/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: 1.41 Å
• R-Value Free: 0.160 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 

Starting Model: experimental

Literature

Crystal structure of shikimate-3-phosphate 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: 95.94 kDa 
• Atom Count: 8,028 
• 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S3P	C [auth A], J [auth B]	SHIKIMATE-3-PHOSPHATE C7 H11 O8 P QYOJSKGCWNAKGW-PBXRRBTRSA-N
1PE	F [auth A], M [auth B], N [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PO4	E [auth A], L [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO3	I [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
FMT	D [auth A], H [auth A], K [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
S3P	BindingDB:  7TM5	Kd: min: 7000, max: 8000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.160 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M37TM5

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.256	α = 90
b = 115.387	β = 90
c = 183.599	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