2D1R Oxidoreductase date Aug 31, 2005
title Crystal Structure Of The Thermostable Japanese Firefly Luciferase Complexed With Oxyluciferin And Amp
authors T.Nakatsu, S.Ichiyama, J.Hiratake, A.Saldanha, N.Kobashi, K.Sakata, H.Kato, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Luciferin 4-Monooxygenase
Chain: A
Synonym: Luciferase
Engineered: Yes
Mutation: Yes
Organism_scientific: Luciola Cruciata
Organism_common: Japanese Firefly
Organism_taxid: 7051
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb101
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc18
symmetry Space Group: P 21 21 21
R_factor 0.184 R_Free 0.210
length a length b length c angle alpha angle beta angle gamma
57.612 181.402 52.743 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand AMP, CSO, OLU enzyme Oxidoreductase E.C. BRENDA

Primary referenceStructural basis for the spectral difference in luciferase bioluminescence., Nakatsu T, Ichiyama S, Hiratake J, Saldanha A, Kobashi N, Sakata K, Kato H, Nature. 2006 Mar 16;440(7082):372-6. PMID:16541080
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (101 Kb) [Save to disk]
  • Biological Unit Coordinates (2d1r.pdb1.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 2D1R
  • CSU: Contacts of Structural Units for 2D1R
  • Likely Quarternary Molecular Structure file(s) for 2D1R
  • Structure Factors (566 Kb)
  • Retrieve 2D1R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D1R from S2C, [Save to disk]
  • Re-refined 2d1r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D1R 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 2D1R
  • 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 2D1R, from MSDmotif at EBI
  • Fold representative 2d1r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d1r] [2d1r_A]
  • SWISS-PROT database: [P13129]
  • Domain organization of [LUCI_LUCCR] by SWISSPFAM
  • Other resources with information on 2D1R
  • Community annotation for 2D1R 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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