3GIX

Crystal structure of human splicing factor dim2

• PDB DOI: https://doi.org/10.2210/pdb3GIX/pdb

• Classification: SPLICING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-06 Released: 2010-03-16 
• Deposition Author(s): Jin, T.C., Guo, F., Zhang, Y.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.197 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 

Starting Model: experimental

Literature

Crystal structure of human splicing factor dim2

Jin, T.C., Guo, F., Wang, Y.T., Howard, A., Zhang, Y.Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.26 kDa 
• Atom Count: 2,861 
• Modelled Residue Count: 282 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin-like protein 4B	A, B	149	Homo sapiens	Mutation(s): 0  Gene Names: DIM2, DLP, TXNL4B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX01 (Homo sapiens) Explore Q9NX01  Go to UniProtKB:  Q9NX01
PHAROS:  Q9NX01 GTEx:  ENSG00000140830

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.197 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.325	α = 90
b = 63.64	β = 92.29
c = 51.148	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Jin, T.C., Guo, F., Zhang, Y.Z.

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-06
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary