3G0H Hydrolase Rna date Jan 28, 2009
title Human Dead-Box Rna Helicase Ddx19, In Complex With An Atp-An Rna
authors T.Karlberg, L.Lehtio, R.Collins, C.H.Arrowsmith, H.Berglund, C.Bo L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Ham A.Johansson, I.Johansson, T.Kotenyova, M.Moche, M.E.Nilsson, P.N T.Nyman, C.Persson, J.Sagemark, P.Schutz, M.I.Siponen, A.G.Thors L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Welin, M.Wisniewska, H.Schuler, Structural Genomics Consortium (Sgc)
compound source
Molecule: Atp-Dependent Rna Helicase Ddx19b
Chain: A
Fragment: Unp Residues 54-275
Synonym: Dead Box Protein 19b, Dead Box Rna Helicase Dead5
Ec: 3.6.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dbp5, Ddx19, Ddx19b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Gold Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4

Molecule: 5'-R(Pupupupupupupu)-3'
Chain: E
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.217 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.570 81.080 124.740 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand ANP, GOL, MG enzyme Hydrolase E.C.3.6.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe DEXD/H-box RNA Helicase DDX19 Is Regulated by an {alpha}-Helical Switch., Collins R, Karlberg T, Lehtio L, Schutz P, van den Berg S, Dahlgren LG, Hammarstrom M, Weigelt J, Schuler H, J Biol Chem. 2009 Apr 17;284(16):10296-300. Epub 2009 Feb 25. PMID:19244245
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (3g0h.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 3G0H
  • CSU: Contacts of Structural Units for 3G0H
  • Likely Quarternary Molecular Structure file(s) for 3G0H
  • Structure Factors (101 Kb)
  • Retrieve 3G0H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3G0H from S2C, [Save to disk]
  • Re-refined 3g0h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3G0H 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 3G0H
  • 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 3G0H, from MSDmotif at EBI
  • Fold representative 3g0h from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3g0h_A] [3g0h_E] [3g0h]
  • SWISS-PROT database: [Q9UMR2]
  • Belongs to the eukaryotic nuclear pore complex (e-npc) family according to TCDB.
  • Domain organization of [DD19B_HUMAN] by SWISSPFAM
  • Domains found in 3G0H: [DEXDc] [HELICc ] by SMART
  • Other resources with information on 3G0H
  • Community annotation for 3G0H 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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