1MHK | pdb_00001mhk

Crystal Structure Analysis of a 26mer RNA molecule, representing a new RNA motif, the hook-turn

• PDB DOI: https://doi.org/10.2210/pdb1MHK/pdb
• NAKB: 1MHK

• Classification: RNA
• Mutation(s): No 


• Deposited: 2002-08-20 Released: 2002-09-06 
• Deposition Author(s): Szep, S., Wang, J., Moore, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.270 (Depositor) 
• R-Value Work: 
  0.239 (Depositor) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of a 26-nucleotide RNA containing a hook-turn

Szep, S., Wang, J., Moore, P.B.

(2003) RNA 9: 44-51

• PubMed: 12554875 
• DOI: https://doi.org/10.1261/rna.2107303
• Primary Citation Related Structures: 
  1MHK


• PubMed Abstract: 
  

  A crystal structure has been obtained for a 26-nucleotide RNA that contains the loop E sequence from Chromatium minutissimum. Rather than having a loop E-like conformation, it consists of an A-form helix that splits into two separate strands following a sheared A-G base pair. The backbone of the strand containing the G of the A-G pair makes a turn of almost 180 degrees in the space of two nucleotides, and then interacts with the minor groove of the helix from which it originates. Similar structures, which we call hook-turns, occur in 16S and 23S rRNAs. They are found at places where the two strands of a helix separate at an A/G juxtaposition to interact with other sequences.

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Organizational Affiliation: 
• Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.37 kDa 
• Atom Count: 570 
• Modeled Residue Count: 26 
• Deposited Residue Count: 26 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA 12-mer BCh12	A [auth S]	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA 14-mer BCh12	B [auth L]	14	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	C [auth S]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.270 (Depositor) 
• R-Value Work:  0.239 (Depositor) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.169	α = 90
b = 62.51	β = 98.76
c = 50.933	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-09-06 
Deposition Author(s): Szep, S., Wang, J., Moore, P.B.

Revision History  

• Version 1.0: 2002-09-06
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description