3B7G Hydrolase date Oct 30, 2007
title Human Dead-Box Rna Helicase Ddx20, Conserved Domain I (Dead) Complex With Amppnp (Adenosine-(Beta,Gamma)-Imidotriphospha
authors T.Karlberg, L.Tresaugues, C.H.Arrowsmith, H.Berglund, R.D.Busam, R.Collins, L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Gras M.Hammarstrom, I.Johansson, A.Kallas, T.Kotenyova, L.Lehtio, M.M M.E.Nilsson, P.Nordlund, T.Nyman, C.Persson, J.Sagemark, L.Svens A.G.Thorsell, S.Van Den Berg, J.Weigelt, M.Welin, L.Holmberg-Sc Structural Genomics Consortium (Sgc)
compound source
Molecule: Probable Atp-Dependent Rna Helicase Ddx20
Chain: A, B
Fragment: Dead Domain
Synonym: Dead Box Protein 20, Dead Box Protein Dp 103, Comp Gems 3, Gemin-3;
Ec: 3.6.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddx20, Dp103, Gemin3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Gold Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic-Bsa4
symmetry Space Group: P 31 2 1
R_factor 0.172 R_Free 0.202
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.560 63.560 214.600 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
ligand ANP enzyme Hydrolase E.C.3.6.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceComparative structural analysis of human DEAD-box RNA helicases., Schutz P, Karlberg T, van den Berg S, Collins R, Lehtio L, Hogbom M, Holmberg-Schiavone L, Tempel W, Park HW, Hammarstrom M, Moche M, Thorsell AG, Schuler H, PLoS One. 2010 Sep 30;5(9). pii: e12791. PMID:20941364
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (3b7g.pdb1.gz) 38 Kb
  • Biological Unit Coordinates (3b7g.pdb2.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 3B7G
  • CSU: Contacts of Structural Units for 3B7G
  • Structure Factors (290 Kb)
  • Retrieve 3B7G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3B7G from S2C, [Save to disk]
  • Re-refined 3b7g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3B7G 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 3B7G
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3B7G, from MSDmotif at EBI
  • Fold representative 3b7g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3b7g] [3b7g_A] [3b7g_B]
  • SWISS-PROT database: [Q9UHI6]
  • Domain organization of [DDX20_HUMAN] by SWISSPFAM
  • Domain found in 3B7G: [DEXDc ] by SMART
  • Other resources with information on 3B7G
  • Community annotation for 3B7G 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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