3NVS

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.02 Å
R-Value Free: 0.138
R-Value Work: 0.114
R-Value Observed: 0.115

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KRB0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S3P Query on S3P Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SHIKIMATE-3-PHOSPHATE C₇ H₁₁ O₈ P QYOJSKGCWNAKGW-PBXRRBTRSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
SKM Query on SKM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID C₇ H₁₀ O₅ JXOHGGNKMLTUBP-HSUXUTPPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GPJ Query on GPJ Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYPHOSATE C₃ H₉ N O₅ P XDDAORKBJWWYJS-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.02 Å
R-Value Free: 0.138
R-Value Work: 0.114
R-Value Observed: 0.115
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m33nvs

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-07-21

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

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