3QJP | pdb_00003qjp

An RAMP protein binding different RNA substrates

• PDB DOI: https://doi.org/10.2210/pdb3QJP/pdb
• NAKB: 3QJP

• 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: 3.30 Å
• R-Value Free: 
  0.272 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.231 (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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 30.44 kDa 
• Atom Count: 2,116 
• Modeled Residue Count: 248 
• Deposited Residue Count: 250 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein PH0350	B [auth A]	242	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: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*AP*GP*UP*UP*UP*AP*A)-3')	A [auth R]	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.272 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.781	α = 90
b = 76.781	β = 90
c = 193.078	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

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