8DTE

Crystal Structure of a toluene tolerance periplasmic transport protein from Neisseria gonorrhoeae

• PDB DOI: https://doi.org/10.2210/pdb8DTE/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Neisseria gonorrhoeae NCCP11945
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-07-25 Released: 2022-08-10 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Starting Model: in silico

Literature

Crystal Structure of a toluene tolerance periplasmic transport protein from Neisseria gonorrhoeae

DeBouver, N.D., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 20.11 kDa 
• Atom Count: 1,391 
• Modelled Residue Count: 172 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic transport protein	A	183	Neisseria gonorrhoeae NCCP11945	Mutation(s): 0  Gene Names: NGK_2593
UniProt
Find proteins for B4RRD5 (Neisseria gonorrhoeae (strain NCCP11945)) Explore B4RRD5  Go to UniProtKB:  B4RRD5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.76	α = 90
b = 51.76	β = 90
c = 167.57	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2024-02-14
  Changes: Data collection
• Version 1.2: 2024-04-03
  Changes: Refinement description