2F5O Hydrolase Dna date Nov 26, 2005
title Mutm Crosslinked To Undamaged Dna Sampling G:C Base Pair Ic3
authors A.Banerjee, W.L.Santos, G.L.Verdine
compound source
Molecule: 5'-D(Apgpgptpapgpaptpcpcpgpgpapcpg
Chain: B
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Dna

Molecule: 5'-D(Tpgpcgptpcpcpgpgpaptpcptpapcp
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna With A Backbone Modification Containiing A Dsulfide Linker;

Molecule: Formamidopyrimidine-Dna Glycosidase
Chain: A
Synonym: Mutm
Ec: 3.2.2.23
Engineered: Yes
Mutation: Yes

Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl-21 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24b
symmetry Space Group: P 21 21 21
R_factor 0.203 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.543 93.253 105.257 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand GOL, ZN enzyme Hydrolase E.C.3.2.2.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of a DNA glycosylase searching for lesions., Banerjee A, Santos WL, Verdine GL, Science. 2006 Feb 24;311(5764):1153-7. PMID:16497933
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (2f5o.pdb1.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 2F5O
  • CSU: Contacts of Structural Units for 2F5O
  • Likely Quarternary Molecular Structure file(s) for 2F5O
  • Structure Factors (200 Kb)
  • Retrieve 2F5O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2F5O from S2C, [Save to disk]
  • Re-refined 2f5o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2F5O 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 2F5O
  • 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
  • 3D motif for 2F5O, from MSDmotif at EBI
  • Fold representative 2f5o from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2f5o_A] [2f5o_C] [2f5o_B] [2f5o]
  • SWISS-PROT database: [P84131]
  • Domain organization of [P84131_BACST] by SWISSPFAM
  • Domains found in 2F5O: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 2F5O
  • Community annotation for 2F5O at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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