1QY3 Luminescent Protein date Sep 09, 2003
title Crystal Structure Of Precyclized Intermediate For The Green Fluorescent Protein R96a Variant (B)
authors D.P.Barondeau, C.D.Putnam, C.J.Kassmann, J.A.Tainer, E.D.Getzoff
compound source
Molecule: Green-Fluorescent Protein
Chain: A
Fragment: Residues 1-229
Engineered: Yes
Mutation: Yes
Organism_scientific: Aequorea Victoria
Organism_taxid: 6100
Gene: Gfp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm109
Expression_system_vector_type: Plasmid
Expression_system_vector: Pken2
symmetry Space Group: P 21 21 21
R_factor 0.203 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.433 62.650 70.976 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
related structures by homologous chain: 1QXT, 2EMD
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures., Barondeau DP, Putnam CD, Kassmann CJ, Tainer JA, Getzoff ED, Proc Natl Acad Sci U S A 2003 Oct 14;100(21):12111-6. Epub 2003 Oct 1. PMID:14523232
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (1qy3.pdb1.gz) 40 Kb
  • CSU: Contacts of Structural Units for 1QY3
  • Likely Quarternary Molecular Structure file(s) for 1QY3
  • Structure Factors (244 Kb)
  • Retrieve 1QY3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QY3 from S2C, [Save to disk]
  • Re-refined 1qy3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1QY3 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 1QY3
  • 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 1QY3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1qy3a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1qy3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1qy3_A] [1qy3]
  • SWISS-PROT database: [P42212]
  • Domain organization of [GFP_AEQVI] by SWISSPFAM
  • Other resources with information on 1QY3
  • Community annotation for 1QY3 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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