1NG3 Oxidoreductase date Dec 16, 2002
title Complex Of Thio (Glycine Oxidase) With Acetyl-Glycine
authors E.C.Settembre, P.C.Dorrestein, J.Park, A.Augustine, T.P.Begley, S
compound source
Molecule: Glycine Oxidase
Chain: A, B
Ec: 1.5.3.-
Engineered: Yes
 Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Gene: Goxb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet16-B
symmetry Space Group: P 61 2 2
R_factor 0.208 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
139.378 139.378 208.155 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand AAC, FAD, PO4 enzyme Oxidoreductase E.C.1.5.3 BRENDA
related structures by homologous chain: 1NG4
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural and mechanistic studies on ThiO, a glycine oxidase essential for thiamin biosynthesis in Bacillus subtilis., Settembre EC, Dorrestein PC, Park JH, Augustine AM, Begley TP, Ealick SE, Biochemistry 2003 Mar 18;42(10):2971-81. PMID:12627963
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (124 Kb) [Save to disk]
  • Biological Unit Coordinates (1ng3.pdb1.gz) 234 Kb
  • LPC: Ligand-Protein Contacts for 1NG3
  • CSU: Contacts of Structural Units for 1NG3
  • Likely Quarternary Molecular Structure file(s) for 1NG3
  • Structure Factors (403 Kb)
  • Retrieve 1NG3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NG3 from S2C, [Save to disk]
  • Re-refined 1ng3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1NG3 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 1NG3
  • 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 1NG3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ng3a1, region A:1-218,A:307-364 [Jmol] [rasmolscript] [script source]
        - Domain d1ng3a2, region A:219-306 [Jmol] [rasmolscript] [script source]
        - Domain d1ng3b1, region B:1-218,B:307-364 [Jmol] [rasmolscript] [script source]
        - Domain d1ng3b2, region B:219-306 [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: [1ng3] [1ng3_B] [1ng3_A]
  • SWISS-PROT database: [O31616]
  • Domain organization of [GLOX_BACSU] by SWISSPFAM
    • Other resources with information on 1NG3
  • Community annotation for 1NG3 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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