3QJL | pdb_00003qjl

One RAMP protein binding different RNA substrates

• PDB DOI: https://doi.org/10.2210/pdb3QJL/pdb
• NAKB: 3QJL

• Classification: IMMUNE SYSTEM/RNA
• Organism(s): Pyrococcus horikoshii
• Mutation(s): No 


• Deposited: 2011-01-30 Released: 2012-02-08 
• Deposition Author(s): Wang, R., Zheng, H., Preamplume, G., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.264 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Cooperative and Specific Binding of a RAMP Protein to Single-stranded CRISPR Repeat RNA

Wang, R., Zheng, H., Preamplume, G., Li, H.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.82 kDa 
• Atom Count: 4,443 
• Modeled Residue Count: 504 
• Deposited Residue Count: 510 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein PH0350	A, C [auth B]	243	Pyrococcus horikoshii	Mutation(s): 0  Gene Names: PH0350
UniProt
Find proteins for O58088 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58088  Go to UniProtKB:  O58088

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*UP*UP*AP*CP*AP*AP*UP*AP*AP*GP*A)-3')	B [auth X], D [auth R]	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.264 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.773	α = 90
b = 88.773	β = 90
c = 257.629	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-08 
Deposition Author(s): Wang, R., Zheng, H., Preamplume, G., Li, H.

Revision History  

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2024-02-21
  Changes: Data collection, Database references