3G00 Hydrolase Dna date Jan 27, 2009
title Mth0212 In Complex With A 9bp Blunt End Dsdna At 1.7 Angstro
authors K.Lakomek, A.Dickmanns, R.Ficner
compound source
Molecule: Exodeoxyribonuclease
Chain: A, B
Synonym: Mth0212
Ec: 3.1.11.2
Engineered: Yes
Mutation: Yes
Organism_scientific: Methanothermobacter Thermautotrophicus
Organism_taxid: 187420
Strain: Delta H (Dsm 1053)
Gene: Mth0212, Mth212, Mth_212
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet_b_001-Mth212 (D151n)

Molecule: 5'-D(Cpgptpaptptpapcpg)-3'
Chain: H
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Cpgptpapuptpapcpg)-3'
Chain: I
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.167 R_Free 0.217
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.966 79.510 87.750 90.00 97.76 90.00
method X-Ray Diffractionresolution 1.74 Å
ligand GOL, MPD, PO4 enzyme Hydrolase E.C.3.1.11.2 BRENDA
Gene MTH
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity


  • Primary referenceCrystal structure analysis of DNA uridine endonuclease Mth212 bound to DNA., Lakomek K, Dickmanns A, Ciirdaeva E, Schomacher L, Ficner R, J Mol Biol. 2010 Jun 18;399(4):604-17. Epub 2010 Apr 29. PMID:20434457
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (3g00.pdb1.gz) 107 Kb
  • LPC: Ligand-Protein Contacts for 3G00
  • CSU: Contacts of Structural Units for 3G00
  • Structure Factors (457 Kb)
  • Retrieve 3G00 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3G00 from S2C, [Save to disk]
  • Re-refined 3g00 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3G00 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 3G00
  • 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
  • 3D motif for 3G00, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3g00_A] [3g00_I] [3g00_H] [3g00] [3g00_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3G00
  • Community annotation for 3G00 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science