8I3X | pdb_00008i3x

Rice APIP6-RING homodimer

• PDB DOI: https://doi.org/10.2210/pdb8I3X/pdb

• Classification: TRANSFERASE
• Organism(s): Oryza sativa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-18 Released: 2023-11-29 
• Deposition Author(s): Zheng, Y., Zhang, X., Liu, Y., Liu, J., Wang, D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of rice APIP6 reveals a new dimerization mode of RING-type E3 ligases that facilities the construction of its working model

Zheng, Y., Zhang, X., Liu, Y., Zhu, T., Wu, X., Ning, Y., Liu, J., Wang, D.

(2023) Phytopathol Res 5

• DOI: https://doi.org/10.1186/s42483-023-00186-w

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: equilibrium centrifugation

Macromolecule Content

• Total Structure Weight: 15.93 kDa 
• Atom Count: 986 
• Modelled Residue Count: 120 
• Deposited Residue Count: 142 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RING-type domain-containing protein	A, B	71	Oryza sativa	Mutation(s): 0  Gene Names: OsI_18510
UniProt
Find proteins for B8AY66 (Oryza sativa subsp. indica) Explore B8AY66  Go to UniProtKB:  B8AY66

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.239	α = 90
b = 46.577	β = 90
c = 83.182	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Zheng, Y., Zhang, X., Liu, Y., Liu, J., Wang, D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32030089

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release