3CNL

Crystal structure of GNP-bound YlqF from T. maritima

• PDB DOI: https://doi.org/10.2210/pdb3CNL/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-26 Released: 2008-06-24 
• Deposition Author(s): Kim, D.J., Jang, J.Y., Yoon, H.-J., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.284 
• R-Value Work: 0.227 
• R-Value Observed: 0.233 

Literature

Crystal structure of YlqF, a circularly permuted GTPase: Implications for its GTPase activation in 50 S ribosomal subunit assembly

Kim, D.J., Jang, J.Y., Yoon, H.-J., Suh, S.W.

(2008) Proteins 72: 1363-1370

• PubMed: 18536017 
• DOI: https://doi.org/10.1002/prot.22112
• Primary Citation of Related Structures:  
  3CNL, 3CNN, 3CNO

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Organizational Affiliation: 

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea.

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: 30.16 kDa 
• Atom Count: 2,032 
• Modelled Residue Count: 233 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	262	Thermotoga maritima	Mutation(s): 0  Gene Names: TM_0768
UniProt
Find proteins for Q9WZM6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZM6  Go to UniProtKB:  Q9WZM6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.284 
• R-Value Work: 0.227 
• R-Value Observed: 0.233 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.132	α = 90
b = 75.15	β = 90
c = 104.919	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-24 
Deposition Author(s): Kim, D.J., Jang, J.Y., Yoon, H.-J., Suh, S.W.

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations