3EBL Hydrolase Receptor date Aug 28, 2008
title Crystal Structure Of Rice Gid1 Complexed With Ga4
authors A.Shimada, T.Nakatsu, M.Ueguchi-Tanaka, H.Kato, M.Matsuoka
compound source
Molecule: Gibberellin Receptor Gid1
Chain: A, B, C, D, E, F
Synonym: Gibberellin-Insensitive Dwarf Protein 1, Protein G Insensitive Dwarf1;
Ec: 3.-.-.-
Engineered: Yes
Organism_scientific: Oryza Sativa Subsp. Japonica
Organism_common: Rice
Organism_taxid: 39947
Gene: Gid1, Os05g0407500, Loc_os05g33730, Oj1657_h11.10, P0
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)Plys
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11b
symmetry Space Group: P 1 21 1
R_factor 0.200 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.760 133.895 118.886 90.00 104.95 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand GA4, MPD, NO3, PO4 enzyme Hydrolase E.C.3 BRENDA
Gene LOC ; OJ1657
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceStructural basis for gibberellin recognition by its receptor GID1., Shimada A, Ueguchi-Tanaka M, Nakatsu T, Nakajima M, Naoe Y, Ohmiya H, Kato H, Matsuoka M, Nature. 2008 Nov 27;456(7221):520-3. doi: 10.1038/nature07546. PMID:19037316
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (324 Kb) [Save to disk]
  • Biological Unit Coordinates (3ebl.pdb1.gz) 60 Kb
  • Biological Unit Coordinates (3ebl.pdb2.gz) 58 Kb
  • Biological Unit Coordinates (3ebl.pdb3.gz) 55 Kb
  • Biological Unit Coordinates (3ebl.pdb4.gz) 58 Kb
  • Biological Unit Coordinates (3ebl.pdb5.gz) 54 Kb
  • Biological Unit Coordinates (3ebl.pdb6.gz) 55 Kb
  • Biological Unit Coordinates (3ebl.pdb7.gz) 104 Kb
  • Biological Unit Coordinates (3ebl.pdb8.gz) 113 Kb
  • Biological Unit Coordinates (3ebl.pdb9.gz) 108 Kb
  • LPC: Ligand-Protein Contacts for 3EBL
  • CSU: Contacts of Structural Units for 3EBL
  • Likely Quarternary Molecular Structure file(s) for 3EBL
  • Structure Factors (4467 Kb)
  • Retrieve 3EBL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3EBL from S2C, [Save to disk]
  • Re-refined 3ebl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3EBL 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 3EBL
  • 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 3EBL, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ebl_D] [3ebl_F] [3ebl_A] [3ebl_B] [3ebl] [3ebl_C] [3ebl_E]
  • SWISS-PROT database: [Q6L545]
  • Domain organization of [GID1_ORYSJ] by SWISSPFAM
  • Other resources with information on 3EBL
  • Community annotation for 3EBL 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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