3IRC | pdb_00003irc

Crystal structure analysis of dengue-1 envelope protein domain III

• PDB DOI: https://doi.org/10.2210/pdb3IRC/pdb
• Entry: 3IRC supersedes: 3EGP

• Classification: VIRAL PROTEIN
• Organism(s): dengue virus type 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-21 Released: 2009-09-29 
• Deposition Author(s): Nelson, C.A., Kim, T., Warren, J.T., Chruszcz, M., Minor, W., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.221 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.211 (Depositor) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Analysis of the Dengue-1 Envelope Protein Domain III

Nelson, C.A., Kim, T., Warren, J.T., Fremont, D.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 12.08 kDa 
• Atom Count: 866 
• Modeled Residue Count: 104 
• Deposited Residue Count: 108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENVELOPE PROTEIN	A	108	dengue virus type 1	Mutation(s): 0  Gene Names: ENVELOPE
UniProt
Find proteins for Q9J7C6 (Dengue virus type 1) Explore Q9J7C6  Go to UniProtKB:  Q9J7C6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.221 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.211 (Depositor) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.087	α = 90
b = 88.087	β = 90
c = 88.087	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-29 
Deposition Author(s): Nelson, C.A., Kim, T., Warren, J.T., Chruszcz, M., Minor, W., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)
• This entry supersedes: 3EGP

Revision History  

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2022-04-13
  Changes: Advisory, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.5: 2024-11-27
  Changes: Structure summary