1JF9 Lyase date Jun 20, 2001
title Crystal Structure Of Selenocysteine Lyase
authors C.D.Lima, S.K.Burley, New York Sgx Research Center For Structu Genomics (Nysgxrc)
compound source
Molecule: Selenocysteine Lyase
Chain: A
Synonym: Nifscdsb, Selenocysteine Reductase, Selenocystein Lyase, Scl;
Ec: 4.4.1.16
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Nifscsdb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 De3
Expression_system_vector_type: T7 Promoter
Expression_system_plasmid: Pet28b
symmetry Space Group: P 43 21 2
R_factor 0.178 R_Free 0.207
crystal
cell
length a length b length c angle alpha angle beta angle gamma
126.375 126.375 133.578 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand PLP enzyme Lyase E.C.4.4.1.16 BRENDA
related structures by homologous chain: 1KMJ, 1KMK
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceAnalysis of the E. coli NifS CsdB protein at 2.0 A reveals the structural basis for perselenide and persulfide intermediate formation., Lima CD, J Mol Biol 2002 Feb 1;315(5):1199-208. PMID:11827487
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (1jf9.pdb1.gz) 146 Kb
  • LPC: Ligand-Protein Contacts for 1JF9
  • CSU: Contacts of Structural Units for 1JF9
  • Likely Quarternary Molecular Structure file(s) for 1JF9
  • Structure Factors (570 Kb)
  • Retrieve 1JF9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JF9 from S2C, [Save to disk]
  • Re-refined 1jf9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1JF9 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 1JF9
  • 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 1JF9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jf9a_, region A [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: [1jf9] [1jf9_A]
  • SWISS-PROT database: [P77444]
  • Domain organization of [SUFS_ECOLI] by SWISSPFAM
  • Other resources with information on 1JF9
  • Community annotation for 1JF9 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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