5GQ9 | pdb_00005gq9

Crystal structure of Thermus thermophilus Argonaute in complex with g1C siDNA and DNA target

• PDB DOI: https://doi.org/10.2210/pdb5GQ9/pdb
• NAKB: 5GQ9

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Thermus thermophilus HB27, Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-08-06 Released: 2017-08-09 
• Deposition Author(s): Zhao, H., Sheng, G., Wang, Y.
• Funding Organization(s): National Natural Science Foundation of China, Ministry of Science and Technology (China), Strategic Priority Research program of the Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.237 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Thermus thermophilus Argonaute in complex with g1C siDNA and DNA target

Zhao, H., Sheng, G., Wang, Y.

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: 176.32 kDa 
• Atom Count: 11,609 
• Modeled Residue Count: 1,375 
• Deposited Residue Count: 1,444 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermus thermophilus Argonaute	A, D [auth B]	685	Thermus thermophilus HB27	Mutation(s): 0  Gene Names: TT_P0026 EC: 3.1.24
UniProt
Find proteins for Q746M7 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q746M7  Go to UniProtKB:  Q746M7

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')	B [auth C], E	21	Thermus thermophilus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3')	C [auth D], F	16	Thermus thermophilus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.237 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.831	α = 90
b = 116.503	β = 90
c = 161.024	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Zhao, H., Sheng, G., Wang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	91440201
National Natural Science Foundation of China	China	31571335
National Natural Science Foundation of China	China	31400640
Ministry of Science and Technology (China)	China	2014CB910102
Strategic Priority Research program of the Chinese Academy of Sciences	China	XDB08010203

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-10-18
  Changes: Author supporting evidence, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description