3RFC Ligase date Apr 06, 2011
title Crystal Structure Of D-Alanine-D-Alanine Ligase A From Xanth Oryzae Pathovar Oryzae With Adp
authors T.T.N.Doan, J.K.Kim, Y.J.Ahn, L.W.Kang
compound source
Molecule: D-Alanine--D-Alanine Ligase 1
Chain: A
Synonym: D-Alanine-D-Alanine Ligase A, D-Ala-D-Ala Ligase 1 Alanylalanine Synthetase 1;
Ec: 6.3.2.4
Engineered: Yes
Mutation: Yes
Organism_scientific: Xanthomonas Oryzae Pv. Oryzae
Organism_taxid: 342109
Strain: Maff 311018
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Modified Pet11a
symmetry Space Group: P 43 21 2
R_factor 0.205 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.236 83.236 98.277 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand ADP, MG enzyme Ligase E.C.6.3.2.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (3rfc.pdb1.gz) 109 Kb
  • LPC: Ligand-Protein Contacts for 3RFC
  • CSU: Contacts of Structural Units for 3RFC
  • Structure Factors (307 Kb)
  • Retrieve 3RFC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RFC from S2C, [Save to disk]
  • Re-refined 3rfc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RFC 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 3RFC
  • 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 3RFC, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rfc] [3rfc_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3RFC
  • Community annotation for 3RFC 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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