6IE7

Crystal structure of ADCP1 tandem Agenet domain 1-2 in complex with H3K9me2

• PDB DOI: https://doi.org/10.2210/pdb6IE7/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: 0.256 
• R-Value Work: 0.190 
• R-Value Observed: 0.194 

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)

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: 75.13 kDa 
• Atom Count: 4,711 
• Modelled Residue Count: 568 
• Deposited Residue Count: 652 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agenet domain-containing protein	A, C [auth B], E [auth C], G [auth D]	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
H3K9me2 peptide	B [auth E], D [auth F], F [auth G], H	11	Arabidopsis thaliana	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NH4	I [auth A], J [auth B], K [auth C], L [auth D]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	B [auth E], D [auth F], F [auth G], H	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.256 
• R-Value Work: 0.190 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.472	α = 90
b = 111.338	β = 90.63
c = 68.144	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
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