1YRX Transcription date Feb 05, 2005
title Structure Of A Novel Photoreceptor: The Bluf Domain Of Appa Rhodobacter Sphaeroides
authors S.Anderson, V.Dragnea, S.Masuda, J.Ybe, K.Moffat, C.Bauer
compound source
Molecule: Hypothetical Protein Rsph03001874
Chain: A, B, C
Fragment: Sequence Database Residues 17-133
Synonym: Appa Bluf Domain
Engineered: Yes
 Organism_scientific: Rhodobacter Sphaeroides 2.4.1
Organism_taxid: 272943
Strain: Atcc 17023 2.4.1 Ncib 8253 Dsm 158
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 41 21 2
R_factor 0.241 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.671 98.671 127.453 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand D9G, FMN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceStructure of a Novel Photoreceptor, the BLUF Domain of AppA from Rhodobacter sphaeroides(,)., Anderson S, Dragnea V, Masuda S, Ybe J, Moffat K, Bauer C, Biochemistry 2005 Jun 7;44(22):7998-8005. PMID:15924418
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (1yrx.pdb1.gz) 41 Kb
  • Biological Unit Coordinates (1yrx.pdb2.gz) 39 Kb
  • Biological Unit Coordinates (1yrx.pdb3.gz) 78 Kb
  • Biological Unit Coordinates (1yrx.pdb4.gz) 117 Kb
  • LPC: Ligand-Protein Contacts for 1YRX
  • CSU: Contacts of Structural Units for 1YRX
  • Likely Quarternary Molecular Structure file(s) for 1YRX
  • Structure Factors (271 Kb)
  • Retrieve 1YRX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YRX from S2C, [Save to disk]
  • Re-refined 1yrx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1YRX 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 1YRX
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1YRX, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yrx_A] [1yrx_B] [1yrx] [1yrx_C]
  • SWISS-PROT database: [Q53119]
  • Domain organization of [Q53119_RHOSH] by SWISSPFAM
  • Domain found in 1YRX: [BLUF ] by SMART
    • Other resources with information on 1YRX
  • Community annotation for 1YRX 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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