2VCK Oxidoreductase date Sep 25, 2007
title Structure Of Phycoerythrobilin Synthase Pebs From The Cyanop Ssm2 In Complex With The Bound Substrate Biliverdin Ixa
authors T.Dammeyer, E.Hofmann, N.Frankenberg-Dinkel
compound source
Molecule: Cyanobacterial Phycoerythrobilin
Chain: A, B, C, D
Synonym: Phycobilin Reductase, Cyanophage Phycoerythrobilin Pebs;
Ec: 1.3.7.6
Engineered: Yes
Organism_scientific: Prochlorococcus Phage P-Ssm2
Organism_taxid: 268746
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pgex-6p-3
symmetry Space Group: P 1
R_factor 0.184 R_Free 0.225
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.560 67.570 81.280 92.26 109.07 106.58
method X-Ray Diffractionresolution 1.80 Å
ligand BLA, MSE enzyme Oxidoreductase E.C.1.3.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referencePhycoerythrobilin synthase (PebS) of a marine virus crystal structures of the biliverdin-complex and the substrate free form., Dammeyer T, Hofmann E, Frankenberg-Dinkel N, J Biol Chem. 2008 Jul 28. PMID:18662988
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (160 Kb) [Save to disk]
  • Biological Unit Coordinates (2vck.pdb1.gz) 40 Kb
  • Biological Unit Coordinates (2vck.pdb2.gz) 41 Kb
  • Biological Unit Coordinates (2vck.pdb3.gz) 41 Kb
  • Biological Unit Coordinates (2vck.pdb4.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 2VCK
  • CSU: Contacts of Structural Units for 2VCK
  • Likely Quarternary Molecular Structure file(s) for 2VCK
  • Structure Factors (670 Kb)
  • Retrieve 2VCK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VCK from S2C, [Save to disk]
  • Re-refined 2vck structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VCK 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 2VCK
  • 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 2VCK, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vck_C] [2vck_D] [2vck_A] [2vck_B] [2vck]
  • SWISS-PROT database: [Q58MU6]
  • Domain organization of [PEBS_BPPRM] by SWISSPFAM
  • Other resources with information on 2VCK
  • Community annotation for 2VCK 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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