4NCB Nuclear Protein Dna date Oct 24, 2013
title Structure Of Thermus Thermophilus Argonaute Bound To Guide D Mer Target Dna With Mg2+
authors G.Sheng, H.Zhao, J.Wang, Y.Rao, Y.Wang
compound source
Molecule: Argonaute
Chain: A, B
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
Strain: Thermophilus
Gene: Argonaute, Tt_p0026
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Sumo

Molecule: 5'-D(Ptpgpapgpgptpapgptpapgpgptptp Papgpt)-3';
Chain: C, E
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Tpaptpapcpapapcpc)-3'
Chain: P, H
Fragment: See Remark 999
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Tpaptpapcpapapcpcptpapcptpapc G)-3';
Chain: D
Fragment: See Remark 999
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Ptpapcptpapcpcptpcpg)-3'
Chain: F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.175 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.736 105.363 92.058 90.00 94.25 90.00
method X-Ray Diffractionresolution 2.19 Å
ligand DT, MG enzyme
Gene TT
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage., Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts DC, van der Oost J, Patel DJ, Wang Y, Proc Natl Acad Sci U S A. 2013 Dec 27. PMID:24374628
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (517 Kb) [Save to disk]
  • Biological Unit Coordinates (4ncb.pdb1.gz) 257 Kb
  • Biological Unit Coordinates (4ncb.pdb2.gz) 255 Kb
  • LPC: Ligand-Protein Contacts for 4NCB
  • CSU: Contacts of Structural Units for 4NCB
  • Structure Factors (1033 Kb)
  • Retrieve 4NCB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NCB from S2C, [Save to disk]
  • Re-refined 4ncb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4NCB in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4NCB
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4NCB, from MSDmotif at EBI
  • Fold representative 4ncb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ncb_E] [4ncb] [4ncb_H] [4ncb_B] [4ncb_D] [4ncb_A] [4ncb_C] [4ncb_P] [4ncb_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4NCB: [Piwi ] by SMART
  • Other resources with information on 4NCB
  • Community annotation for 4NCB at PDBWiki (http://pdbwiki.org)

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