5VRD Oxidoreductase date May 10, 2017
title Crystal Structure For Methylobacterium Extorquens Pqqcd (Nat Fusion)
authors R.L.Evans Iii, C.M.Wilmot, M.A.Esler
compound source
Molecule: Bifunctional Coenzyme Pqq Synthesis Protein Cd
Chain: D, A, B, C
Synonym: Pyrroloquinoline Quinone Biosynthesis Protein Cd
Ec: 1.3.3.11
Engineered: Yes
 Organism_scientific: Methylobacterium Extorquens (Strain At Dsm 1338 Jcm 2805 Ncimb 9133 Am1);
Organism_taxid: 272630
Strain: Atcc 14718 Dsm 1338 Jcm 2805 Ncimb 9133 Am1
Gene: Pqqcd, Mexam1_meta1p1749
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 41 21 2
R_factor 0.253 R_Free 0.327
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.936 103.936 243.485 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand
enzyme Oxidoreductase E.C.1.3.3.11 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (287 Kb) [Save to disk]
  • Biological Unit Coordinates (5vrd.pdb1.gz) 137 Kb
  • Biological Unit Coordinates (5vrd.pdb2.gz) 142 Kb
  • CSU: Contacts of Structural Units for 5VRD
  • Structure Factors (1800 Kb)
  • Retrieve 5VRD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VRD from S2C, [Save to disk]
    • View 5VRD 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 5VRD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vrd_D] [5vrd_B] [5vrd_C] [5vrd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5VRD
  • Community annotation for 5VRD at PDBWiki (http://pdbwiki.org)

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