1B04 Ligase date Nov 16, 1998
title Structure Of The Adenylation Domain Of An Nad+ Dependent Lig
authors M.R.Singleton, K.Hakansson, D.J.Timson, D.B.Wigley
compound source
Molecule: Protein (Dna Ligase)
Chain: A, B
Fragment: Adenylation Domain
Ec: 6.5.1.2
Engineered: Yes
Mutation: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Strain: Nca 1503
Gene: Lig
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21d
Expression_system_gene: Lig
symmetry Space Group: P 43 21 2
R_factor 0.230 R_Free 0.310
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.720 95.720 225.890 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand
enzyme Ligase E.C.6.5.1.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure of the adenylation domain of an NAD+-dependent DNA ligase., Singleton MR, Hakansson K, Timson DJ, Wigley DB, Structure Fold Des 1999 Jan 15;7(1):35-42. PMID:10368271
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (108 Kb) [Save to disk]
  • Biological Unit Coordinates (1b04.pdb1.gz) 51 Kb
  • Biological Unit Coordinates (1b04.pdb2.gz) 52 Kb
  • CSU: Contacts of Structural Units for 1B04
  • Likely Quarternary Molecular Structure file(s) for 1B04
  • Structure Factors (202 Kb)
  • Retrieve 1B04 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1B04 from S2C, [Save to disk]
  • Re-refined 1b04 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1B04 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 1B04
  • 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 1B04, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1b04a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1b04b_, region B [Jmol] [rasmolscript] [script source]
  • 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: [1b04_A] [1b04] [1b04_B]
  • SWISS-PROT database: [O87703]
  • Domain organization of [DNLJ_BACST] by SWISSPFAM
  • Domain found in 1B04: [LIGANc ] by SMART
  • Other resources with information on 1B04
  • Community annotation for 1B04 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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