5CO8 Hydrolase date Jul 20, 2015
title Crystal Structure Of The Holliday Junction-Resolving Enzyme In Complex With Product Dna And Mg2+ Ion
authors Y.J.Liu, A.D.J.Freeman, A.C.Declais, T.J.Wilson, A.Gartner, D.M.J
compound source
Molecule: Dna (31-Mer)
Chain: R
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Nuclease-Like Protein
Chain: C
Engineered: Yes

Organism_scientific: Chaetomium Thermophilum (Strain Dsm 14 144.50 Imi 039719);
Organism_taxid: 759272
Strain: Dsm 1495 Cbs 144.50 Imi 039719
Gene: Ctht_0007290
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Apgpapcptpgpcpapgptptpgpap 3');
Chain: X
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Nuclease-Like Protein
Chain: A
Engineered: Yes

Organism_scientific: Chaetomium Thermophilum (Strain Dsm 14 144.50 Imi 039719);
Organism_taxid: 759272
Strain: Dsm 1495 Cbs 144.50 Imi 039719
Gene: Ctht_0007290
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Tpgpapgpcpgpgptpgpgptptpgp 3');
Chain: H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 31 2 1
R_factor 0.239 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.072 98.072 119.571 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand MG, MSE enzyme
Gene CTHT
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceCrystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA., Liu Y, Freeman AD, Declais AC, Wilson TJ, Gartner A, Lilley DM, Cell Rep. 2015 Dec 22;13(11):2565-75. doi: 10.1016/j.celrep.2015.11.042. Epub, 2015 Dec 10. PMID:26686639
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (159 Kb) [Save to disk]
  • Biological Unit Coordinates (5co8.pdb1.gz) 151 Kb
  • LPC: Ligand-Protein Contacts for 5CO8
  • CSU: Contacts of Structural Units for 5CO8
  • Structure Factors (2099 Kb)
  • Retrieve 5CO8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CO8 from S2C, [Save to disk]
  • Re-refined 5co8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CO8 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 5CO8
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5co8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5co8_X] [5co8_H] [5co8_A] [5co8_C] [5co8_R] [5co8]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5CO8: [HhH2] [XPGI] [XPGN ] by SMART
  • Other resources with information on 5CO8
  • Community annotation for 5CO8 at PDBWiki (http://pdbwiki.org)

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