1BGB Hydrolase Dna date May 28, 1998
title Ecorv Endonuclease Complex With 5'-Cgggatatccc Dna
authors J.Perona, N.C.Horton
compound source
Molecule: Dna (5'-D(Cpgpgpgpaptpaptpcpcpc)-3')
Chain: C, D
Engineered: Yes
Synthetic: Yes

Molecule: Ecorv Endonuclease
Chain: A, B
Ec: 3.1.21.4
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.184 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.400 50.200 64.100 96.00 109.00 108.00
method X-Ray Diffractionresolution 2.00 Å
ligand
enzyme Hydrolase E.C.3.1.21.4 BRENDA
related structures by homologous chain: 1AZ0, 1BSU, 1EO3
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity


  • Primary referenceRecognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts., Horton NC, Perona JJ, J Biol Chem 1998 Aug 21;273(34):21721-9. PMID:9705308
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (1bgb.pdb1.gz) 86 Kb
  • CSU: Contacts of Structural Units for 1BGB
  • Likely Quarternary Molecular Structure file(s) for 1BGB
  • Retrieve 1BGB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BGB from S2C, [Save to disk]
  • View 1BGB 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 1BGB
  • 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
  • 3D motif for 1BGB, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bgba_, region A [Jmol] [rasmolscript] [script source]
        - Domain d11bgb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1bgb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1bgb_A] [1bgb_B] [1bgb_C] [1bgb] [1bgb_D]
  • SWISS-PROT database: [P04390]
  • Domain organization of [T2E5_ECOLX] by SWISSPFAM
  • Other resources with information on 1BGB
  • Community annotation for 1BGB 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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