6S48 Hydrolase date Jun 26, 2019
title Avaii Restriction Endonuclease In Complex With Partially Cle
authors M.Kisiala, M.Kowalska, H.Korza, H.Czapinska, M.Bochtler
compound source
Molecule: Type II Site-Specific Deoxyribonuclease
Chain: A, B
Synonym: Avaii Restriction Endonuclease
Engineered: Yes
 Organism_scientific: Nostoc Sp. Pcc 7120 = Fachb-418
Organism_taxid: 103690
Gene: Alr0933
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: Er2566
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet28a
Expression_system_plasmid: Pet28a

Molecule: Dna (5'-D(Gpaptpgpgptpcpcptpapc)-3')
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gptpapg)-3')
Chain: D, H
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgpapcpcpaptpc)-3')
Chain: E, I
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpaptpg)-3')
Chain: F
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgptpcpcptpapc)-3')
Chain: G
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.176 R_Free 0.217
crystal
cell
length a length b length c angle alpha angle beta angle gamma
37.129 116.210 56.774 90.00 102.91 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand 1PE, BME, CA, PGE, SER enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceRestriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation., Kisiala M, Kowalska M, Pastor M, Korza HJ, Czapinska H, Bochtler M, Nucleic Acids Res. 2020 May 27. pii: 5847776. doi: 10.1093/nar/gkaa403. PMID:32459314
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (6s48.pdb1.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 6S48
  • CSU: Contacts of Structural Units for 6S48
  • Structure Factors (328 Kb)
  • Retrieve 6S48 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6S48 from S2C, [Save to disk]
    • View 6S48 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 6S48
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6s48_H] [6s48_C] [6s48_G] [6s48_B] [6s48_E] [6s48_F] [6s48_A] [6s48_D] [6s48_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6S48
  • Community annotation for 6S48 at PDBWiki (http://pdbwiki.org)

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