6IE6 | pdb_00006ie6

Crystal structure of ADCP1 tandem Agenet domain 3-4 in complex with H3K9me2

PDB DOI: https://doi.org/10.2210/pdb6IE6/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.232 (Depositor), 0.252 (DCC)
R-Value Work:
0.186 (Depositor)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

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

Zhao, S., Zhang, B., Li, H.

(2019) Cell Res 29: 54-66

Macromolecule Content

Total Structure Weight: 19.34 kDa
Atom Count: 1,466
Modeled Residue Count: 160
Deposited Residue Count: 170
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agenet domain-containing protein	A	160	Arabidopsis thaliana	Mutation(s): 0 Gene Names: ADCP1
UniProt
Find proteins for Q500V5 (Arabidopsis thaliana) Explore Q500V5 Go to UniProtKB: Q500V5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q500V5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K9me2	B [auth P]	10	Arabidopsis thaliana	Mutation(s): 0

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	B [auth P]	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.232 (Depositor), 0.252 (DCC)
R-Value Work: 0.186 (Depositor)
R-Value Observed: 0.191 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.891	α = 90
b = 56.891	β = 90
c = 210.005	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-01-16

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.