6IE6

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
R-Value Work: 0.186
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

This is version 1.0 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
Modelled Residue Count: 160
Deposited Residue Count: 170
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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
R-Value Work: 0.186
R-Value Observed: 0.191
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

View Full Validation Report

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

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 R01GM133198.