1F9I Signaling Protein date Jul 10, 2000
title Crystal Structure Of The Photoactive Yellow Protein Mutant Y
authors R.Brudler, T.E.Meyer, U.K.Genick, G.Tollin, E.D.Getzoff
compound source
Molecule: Photoactive Yellow Protein
Chain: A
Engineered: Yes
Mutation: Yes
Organism_scientific: Halorhodospira Halophila
Organism_taxid: 1053
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet 20b
symmetry Space Group: P 63
length a length b length c angle alpha angle beta angle gamma
65.699 65.699 40.239 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.10 Å
ligand HC4 enzyme
related structures by homologous chain: 1OTA, 1OTB

Primary referenceCoupling of hydrogen bonding to chromophore conformation and function in photoactive yellow protein., Brudler R, Meyer TE, Genick UK, Devanathan S, Woo TT, Millar DP, Gerwert K, Cusanovich MA, Tollin G, Getzoff ED, Biochemistry 2000 Nov 7;39(44):13478-86. PMID:11063584
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (1f9i.pdb1.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 1F9I
  • CSU: Contacts of Structural Units for 1F9I
  • Likely Quarternary Molecular Structure file(s) for 1F9I
  • Structure Factors (393 Kb)
  • Retrieve 1F9I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1F9I from S2C, [Save to disk]
  • Re-refined 1f9i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1F9I 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 1F9I
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1F9I from the CEP Server.
  • 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 1F9I, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1f9ia_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1f9i 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: [1f9i_A] [1f9i]
  • SWISS-PROT database: [P16113]
  • Domain organization of [PYP_HALHA] by SWISSPFAM
  • Domain found in 1F9I: [PAS ] by SMART
  • Other resources with information on 1F9I
  • Community annotation for 1F9I 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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