6XMV | pdb_00006xmv

The crystal structure of Neisseria gonorrhoeae DolP (NGO1985)

• PDB DOI: https://doi.org/10.2210/pdb6XMV/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Neisseria gonorrhoeae FA 1090, Tequatrovirus T4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-06-30 Released: 2021-11-17 
• Deposition Author(s): Li, J., Peterson Brown, L.E., Reed, R.W., Wierzbicki, I.H., Sikora, A.E., Korotkov, K.V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), 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: 2.75 Å
• R-Value Free: 
  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

The structure and function of a new component of Bam complex in Neisseria

Wierzbicki, I.H., Zielke, R.A., Li, J., Begum, A.A., Baarda, B.I., Peterson Brown, L.E., Reed, R.W., Korotkov, K.V., Jerse, A.E., Sikora, A.E.

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

Macromolecule Content 

• Total Structure Weight: 38.01 kDa 
• Atom Count: 2,437 
• Modeled Residue Count: 307 
• Deposited Residue Count: 339 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolysin,Endolysin	A	339	Neisseria gonorrhoeae FA 1090, Tequatrovirus T4 This entity is chimeric	Mutation(s): 3  Gene Names: NGO_1985, e, T4Tp126 EC: 3.2.1.17
UniProt
Find proteins for D9IEF7 (Enterobacteria phage T4) Explore D9IEF7  Go to UniProtKB:  D9IEF7
Find proteins for Q5F5E4 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F5E4  Go to UniProtKB:  Q5F5E4
UniProt Groups	Q5F5E4D9IEF7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.282 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.04	α = 90
b = 125.9	β = 90
c = 47.92	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Li, J., Peterson Brown, L.E., Reed, R.W., Wierzbicki, I.H., Sikora, A.E., Korotkov, K.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110787
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI117235

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary