6JZN

Structure of the intermembrane space region of PARC6-PDV1

• PDB DOI: https://doi.org/10.2210/pdb6JZN/pdb

• Classification: PROTEIN BINDING
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-02 Released: 2020-05-06 
• Deposition Author(s): Feng, Y., Liu, Z.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.272 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Literature

Structure of PARC6 and PDV1 complex from Arabidopsis thaliana

Feng, Y., Liu, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.78 kDa 
• Atom Count: 4,583 
• Modelled Residue Count: 563 
• Deposited Residue Count: 636 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plastid division protein CDP1, chloroplastic	A [auth C], B, C [auth D], D [auth A]	149	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CDP1, ARC6H, PARC6, At3g19180, MVI11.9
UniProt
Find proteins for Q8VY16 (Arabidopsis thaliana) Explore Q8VY16  Go to UniProtKB:  Q8VY16

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Plastid division protein PDV1	E [auth G], F, G [auth H], H [auth E]	10	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PDV1, At5g53280, K19E1.8
UniProt
Find proteins for Q9FK13 (Arabidopsis thaliana) Explore Q9FK13  Go to UniProtKB:  Q9FK13

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.272 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.454	α = 90
b = 95.827	β = 90
c = 196.566	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): Feng, Y., Liu, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31822012
National Natural Science Foundation of China	China	31670766
National Natural Science Foundation of China		31400635

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description