4XAI

Crystal Structure of red flour beetle NR2E1/TLX

• PDB DOI: https://doi.org/10.2210/pdb4XAI/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli O157:H7, Tribolium castaneum, Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-12-14 Released: 2015-03-04 
• Deposition Author(s): Zhi, X., Zhou, E., Xu, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.262 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

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

Macromolecule Content

• Total Structure Weight: 132.78 kDa 
• Atom Count: 9,306 
• Modelled Residue Count: 1,169 
• Deposited Residue Count: 1,188 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Tailless ortholog	A, C [auth B]	573	Escherichia coli O157:H7, Tribolium castaneum This entity is chimeric	Mutation(s): 0  Gene Names: malE, Z5632, ECs5017
UniProt
Find proteins for Q9NCL0 (Tribolium castaneum) Explore Q9NCL0  Go to UniProtKB:  Q9NCL0
Find proteins for P0AEY0 (Escherichia coli O157:H7) Explore P0AEY0  Go to UniProtKB:  P0AEY0
UniProt Groups	P0AEY0Q9NCL0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Grunge, isoform J	B [auth P], D [auth Q]	21	Drosophila melanogaster	Mutation(s): 0  EC: 3.5.1
UniProt
Find proteins for M9PHT1 (Drosophila melanogaster) Explore M9PHT1  Go to UniProtKB:  M9PHT1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	E [auth C], F [auth D]	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	E [auth C], F [auth D]	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.262 
• R-Value Work: 0.207 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.782	α = 90
b = 84.098	β = 90
c = 262.437	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building
O	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Zhi, X., Zhou, E., Xu, E.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary