1JZV | pdb_00001jzv

Crystal structure of a bulged RNA from the SL2 stem-loop of the HIV-1 psi-RNA

• PDB DOI: https://doi.org/10.2210/pdb1JZV/pdb
• NAKB: 1JZV

• Classification: RNA
• Mutation(s): No 


• Deposited: 2001-09-17 Released: 2003-11-11 
• Deposition Author(s): Xiong, Y., Sudarsanakumar, C., Deng, J., Pan, B., Sundaralingam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 

Literature

Crystal Structure of a Bulged RNA from the SL2 Stem-loop of the HIV-1 psi-RNA

Xiong, Y., Sudarsanakumar, C., Deng, J., Pan, M., Sundaralingam, M.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.26 kDa 
• Atom Count: 800 
• Modeled Residue Count: 34 
• Deposited Residue Count: 34 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)-3'	A, C	8	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3'	B, D	9	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.8	α = 90
b = 45.8	β = 90
c = 89.65	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-11 
Deposition Author(s): Xiong, Y., Sudarsanakumar, C., Deng, J., Pan, B., Sundaralingam, M.

Revision History  

• Version 1.0: 2003-11-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations