4LJX | pdb_00004ljx

Crystal structure of an AT-rich interactive domain-containing protein 3A (ARID3A) from Homo sapiens at 2.21 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4LJX/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-07-05 Released: 2013-08-28 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an AT-rich interactive domain-containing protein 3A (ARID3A) from Homo sapiens at 2.21 A resolution

Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 32.52 kDa 
• Atom Count: 2,036 
• Modeled Residue Count: 244 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AT-rich interactive domain-containing protein 3A	A, B	137	Homo sapiens	Mutation(s): 1  Gene Names: ARID3A, BC060828, DRIL1, DRIL3, DRX, E2FBP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99856 (Homo sapiens) Explore Q99856  Go to UniProtKB:  Q99856
PHAROS:  Q99856 GTEx:  ENSG00000116017

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34LJX

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.924	α = 108.12
b = 43.092	β = 82.22
c = 44.894	γ = 98.17

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
PHASER	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Joint Center for Structural Genomics (JCSG), Partnership for Stem Cell Biology (STEMCELL)

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary