1OFD Oxidoreductase date Apr 14, 2003
title Glutamate Synthase From Synechocystis Sp In Complex With 2-Oxoglutarate At 2.0 Angstrom Resolution
authors R.H.H.Van Den Heuvel, A.Mattevi
compound source
Molecule: Ferredoxin-Dependent Glutamate Synthase 2
Chain: A, B
Synonym: Glutamate Synthase
Ec: 1.4.7.1
Engineered: Yes
 Organism_scientific: Synechocystis Sp.
Organism_taxid: 1148
Strain: Pcc6803
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Clr207 Reca
symmetry Space Group: P 21 21 21
R_factor 0.192 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
125.017 149.665 195.926 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand AKG, F3S, FMN enzyme Oxidoreductase E.C.1.4.7.1 BRENDA
related structures by homologous chain: 1OFE
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • glutamate synthase (ferredox...
  • oxidoreductase activity
  • metal ion binding
  • iron-sulfur cluster binding
  • 3 iron, 4 sulfur cluster bin...
  • glutamate biosynthetic proce...
  • glutamine metabolic process
  • nitrogen compound metabolic ...
  • cellular amino acid biosynth...
  • oxidation-reduction process
  • L-glutamate biosynthetic pro...

    • Primary referenceThe active conformation of glutamate synthase and its binding to ferredoxin., van den Heuvel RH, Svergun DI, Petoukhov MV, Coda A, Curti B, Ravasio S, Vanoni MA, Mattevi A, J Mol Biol 2003 Jun 27;330(1):113-28. PMID:12818206
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (492 Kb) [Save to disk]
  • Biological Unit Coordinates (1ofd.pdb1.gz) 246 Kb
  • Biological Unit Coordinates (1ofd.pdb2.gz) 244 Kb
  • LPC: Ligand-Protein Contacts for 1OFD
  • CSU: Contacts of Structural Units for 1OFD
  • Likely Quarternary Molecular Structure file(s) for 1OFD
  • Structure Factors (1913 Kb)
  • Retrieve 1OFD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1OFD from S2C, [Save to disk]
  • Re-refined 1ofd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1OFD 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.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 1OFD
  • 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 1OFD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ofda3, region A:1-430 [Jmol] [rasmolscript] [script source]
        - Domain d1ofda1, region A:1240-1507 [Jmol] [rasmolscript] [script source]
        - Domain d1ofda2, region A:431-1239 [Jmol] [rasmolscript] [script source]
        - Domain d1ofdb3, region B:1-430 [Jmol] [rasmolscript] [script source]
        - Domain d1ofdb1, region B:1240-1507 [Jmol] [rasmolscript] [script source]
        - Domain d1ofdb2, region B:431-1239 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ofd from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ofd_A] [1ofd_B]
  • SWISS-PROT database: [P55038]
  • Domain organization of [GLTS_SYNY3] by SWISSPFAM
  • Alignments of the sequence of 1OFD with the sequences similar proteins can be viewed for 1OFD's classification [GLTS_SYNY3] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [GLTS_SYNY3] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1OFD
  • Community annotation for 1OFD 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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