6DGD Dna Binding Protein Dna date May 17, 2018
title Pria Helicase Bound To Dsdna Of A Dna Replication Fork
authors K.A.Satyshur, T.A.Windgassen, J.L.Keck
compound source
Molecule: Primosomal Protein N'
Chain: A, B
Synonym: Atp-Dependent Helicase Pria
Ec: 3.6.4.-
Engineered: Yes
Organism_scientific: Klebsiella Pneumoniae
Organism_taxid: 573
Gene: Pria, B1727_25905, Cpt10_21250, Samea3304003_04572
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta2
Expression_system_plasmid: Pet28-K.Pneumoniae Pria

Molecule: Dna (5'-D(Papgpcpapcpgpcpcpgpapcpt)-3
Chain: W
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgptpcpgpgpcpgptpgpcptpc)-3
Chain: X, Z
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgpapgpcpapcpgpcpcpgpapcpt
Chain: Y
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.248 R_Free 0.290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.560 106.760 256.830 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.82 Å
ligand SO4, ZN enzyme Hydrolase E.C.3.6.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase., Windgassen TA, Leroux M, Satyshur KA, Sandler SJ, Keck JL, Proc Natl Acad Sci U S A. 2018 Sep 10. pii: 1809842115. doi:, 10.1073/pnas.1809842115. PMID:30201718
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (247 Kb) [Save to disk]
  • Biological Unit Coordinates (6dgd.pdb1.gz) 124 Kb
  • Biological Unit Coordinates (6dgd.pdb2.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 6DGD
  • CSU: Contacts of Structural Units for 6DGD
  • Structure Factors (1826 Kb)
  • Retrieve 6DGD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6DGD from S2C, [Save to disk]
  • View 6DGD 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 6DGD
  • 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
  • Fold representative 6dgd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6dgd_B] [6dgd_Z] [6dgd_Y] [6dgd_W] [6dgd_X] [6dgd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6DGD
  • Community annotation for 6DGD at PDBWiki (http://pdbwiki.org)

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