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), 0.271 (DCC)
R-Value Work:
0.238 (Depositor), 0.238 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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.

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

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| 3D Structure

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... 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KKJ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	E [auth A], H [auth B], K [auth C], M [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	F [auth A], I [auth B], L [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.278 (Depositor), 0.271 (DCC)
R-Value Work: 0.238 (Depositor), 0.238 (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

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Ligand Structure Quality Assessment

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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 (Full details and data files)

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

7NPE | pdb_00007npe

Vibrio cholerae ParA2-ADP

Literature

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

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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