7NPE | pdb_00007npe

Vibrio cholerae ParA2-ADP

• PDB DOI: https://doi.org/10.2210/pdb7NPE/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-02-26 Released: 2021-07-21 
• Deposition Author(s): Parker, A.V., Bergeron, J.R.C.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

The cryo-EM structure of the bacterial type I segregation filament reveals ParA s conformational plasticity upon DNA binding

Parker, A.V., Mann, D., Tzokov, S.B., Hwang, L.C., Bergeron, J.R.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: microscopy

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 187.75 kDa 
• Atom Count: 12,065 
• Modeled Residue Count: 1,602 
• Deposited Residue Count: 1,628 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA family ATPase	A, B, C, D	407	Vibrio cholerae	Mutation(s): 0  Gene Names:  parA, BC353_10845, C9J66_03480, ERS013138_01197, ERS013166_00021, ERS013186_00500, ERS013193_00027, ERS013197_04093, ERS013198_00323, ERS013199_01186, ERS013200_00295, ERS013202_00851, ERS013206_01885, F0315_18570, FLM02_03395, FXF03_20770, HPY05_13545
UniProt
Find proteins for Q9KKJ2 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KKJ2  Go to UniProtKB:  Q9KKJ2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	E [auth A], H [auth B], K [auth C], M [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
GOL	G [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	F [auth A], I [auth B], L [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.205	α = 90
b = 199.205	β = 90
c = 260.066	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Parker, A.V., Bergeron, J.R.C.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 2.0: 2023-10-18
  Type: Coordinate replacement
  Reason: Polymer geometry
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary
• Version 2.1: 2024-01-31
  Changes: Refinement description