3NVS | pdb_00003nvs

1.02 Angstrom resolution crystal structure of 3-phosphoshikimate 1-carboxyvinyltransferase from Vibrio cholerae in complex with shikimate-3-phosphate (partially photolyzed) and glyphosate

• PDB DOI: https://doi.org/10.2210/pdb3NVS/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-07-08 Released: 2010-07-21 
• Deposition Author(s): Minasov, G., Light, S.H., Halavaty, A., Shuvalova, G., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free: 
  0.138 (Depositor), 0.136 (DCC) 
• R-Value Work: 
  0.114 (Depositor), 0.114 (DCC) 
• R-Value Observed: 
  0.115 (Depositor) 

Starting Model: experimental

Literature

1.02 Angstrom Resolution Crystal Structure of 3-Phosphoshikimate 1-Carboxyvinyltransferase from Vibrio cholerae in complex with Shikimate-3-Phosphate (Partially Photolyzed) and Glyphosate

Minasov, G., Light, S.H., Halavaty, A., Shuvalova, G., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Macromolecule Content 

• Total Structure Weight: 50.03 kDa 
• Atom Count: 4,537 
• Modeled Residue Count: 426 
• Deposited Residue Count: 450 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-phosphoshikimate 1-carboxyvinyltransferase	A	450	Vibrio cholerae	Mutation(s): 0  Gene Names: aroA, NP_231368, VC_1732 EC: 2.5.1.19
UniProt
Find proteins for Q9KRB0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KRB0  Go to UniProtKB:  Q9KRB0

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S3P	B [auth A]	SHIKIMATE-3-PHOSPHATE C7 H11 O8 P QYOJSKGCWNAKGW-PBXRRBTRSA-N
EPE	L [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SKM	C [auth A]	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID C7 H10 O5 JXOHGGNKMLTUBP-HSUXUTPPSA-N
GPJ	D [auth A]	GLYPHOSATE C3 H9 N O5 P XDDAORKBJWWYJS-UHFFFAOYSA-O
PO4	M [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	H [auth A], I [auth A], J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.02 Å
• R-Value Free:  0.138 (Depositor), 0.136 (DCC) 
• R-Value Work:  0.114 (Depositor), 0.114 (DCC) 
• R-Value Observed: 0.115 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33nvs

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.866	α = 90
b = 87.484	β = 105.26
c = 49.994	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Minasov, G., Light, S.H., Halavaty, A., Shuvalova, G., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description