2EMD Luminescence date Mar 31, 1997
title Green Fluorescent Protein From Aequorea Victoria, Mutant
authors G.Palm, A.Zdanov, A.Wlodawer
compound source
Molecule: Green Fluorescent Protein
Chain: A
Synonym: Gfp
Engineered: Yes
Mutation: Yes
Organism_scientific: Aequorea Victoria
Organism_taxid: 6100
Organ: Photogenic Organ
Tissue: Circumoral Ring Canal
Gene: Gfp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21, Omega878
Expression_system_cellular_location: Cytoplasm
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet11a
Expression_system_plasmid: Pfred42
Expression_system_gene: Sg42
symmetry Space Group: I 41 3 2
R_factor 0.191 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
175.600 175.600 175.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CSH enzyme
related structures by homologous chain: 1EMG, 1QY3
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe structural basis for spectral variations in green fluorescent protein., Palm GJ, Zdanov A, Gaitanaris GA, Stauber R, Pavlakis GN, Wlodawer A, Nat Struct Biol 1997 May;4(5):361-5. PMID:9145105
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (2emd.pdb1.gz) 76 Kb
  • LPC: Ligand-Protein Contacts for 2EMD
  • CSU: Contacts of Structural Units for 2EMD
  • Likely Quarternary Molecular Structure file(s) for 2EMD
  • Structure Factors (200 Kb)
  • Retrieve 2EMD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2EMD from S2C, [Save to disk]
  • Re-refined 2emd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2EMD 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 2EMD
  • 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 2EMD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2emd__, region [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: [2emd_A] [2emd]
  • SWISS-PROT database: [P42212]
  • Domain organization of [GFP_AEQVI] by SWISSPFAM
  • Other resources with information on 2EMD
  • Community annotation for 2EMD 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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