6IE4 | pdb_00006ie4

Crystal structure of ADCP1 tandem Agenet domain 1-2 in complex with H3K9me1

• PDB DOI: https://doi.org/10.2210/pdb6IE4/pdb

• Classification: TRANSLATION
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-09-13 Released: 2019-01-16 
• Deposition Author(s): Zhao, S., Zhang, B., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

ADCP1-tandem Agenet domain 1-2 in complex wit h H3K9me2

Zhao, S., Zhang, B., Li, H.

(2019) Cell Res 29: 54-66

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: isothermal titration calorimetry

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 37.5 kDa 
• Atom Count: 2,431 
• Modeled Residue Count: 293 
• Deposited Residue Count: 326 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agenet domain-containing protein	A, C	152	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ADCP1
UniProt
Find proteins for Q500V5 (Arabidopsis thaliana) Explore Q500V5  Go to UniProtKB:  Q500V5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K9me1 peptide	B, D	11	Arabidopsis thaliana	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ	B, D	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.515	α = 90
b = 67.529	β = 90
c = 116.679	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Zhao, S., Zhang, B., Li, H.

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Structure summary