1DMU Hydrolase Dna date Dec 15, 1999
title Crystal Structure Of The Restriction Endonuclease Bgli (E.C. Bound To Its Dna Recognition Sequence
authors M.Newman, K.Lunnen, G.Wilson, J.Greci, I.Schildkraut, S.E.V.Phill
compound source
Molecule: Dna (5'- D(Aptpcpgpcpcptpapaptpapgpgpcpgpapt)-3');
Chain: F
Engineered: Yes
Synthetic: Yes
Other_details: Contains Dna Recognition Sequence Of Bgli

Molecule: Bgli Restriction Endonuclease
Chain: A
Ec: 3.1.21.4
Engineered: Yes

Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.177 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.480 81.600 117.060 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand BME, CA enzyme Hydrolase E.C.3.1.21.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • endonuclease activity


  • Primary referenceCrystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence., Newman M, Lunnen K, Wilson G, Greci J, Schildkraut I, Phillips SE, EMBO J 1998 Sep 15;17(18):5466-76. PMID:9736624
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (66 Kb) [Save to disk]
  • Biological Unit Coordinates (1dmu.pdb1.gz) 118 Kb
  • LPC: Ligand-Protein Contacts for 1DMU
  • CSU: Contacts of Structural Units for 1DMU
  • Likely Quarternary Molecular Structure file(s) for 1DMU
  • Structure Factors (131 Kb)
  • Retrieve 1DMU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DMU from S2C, [Save to disk]
  • Re-refined 1dmu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DMU in 3D
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  • 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 1DMU
  • 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 1DMU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dmua_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1dmu 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: [1dmu_A] [1dmu] [1dmu_F]
  • SWISS-PROT database: [O68557]
  • Domain organization of [T2B1_BACSU] by SWISSPFAM
  • Other resources with information on 1DMU
  • Community annotation for 1DMU at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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