2RB4 Hydrolase date Sep 18, 2007
title Crystal Structure Of The Helicase Domain Of Human Ddx25 Rna
authors L.Lehtio, M.Hogbom, J.Uppenberg, C.H.Arrowsmith, H.Berglund, A.M. M.Ehn, S.Flodin, A.Flores, S.Graslund, B.M.Hallberg, M.Hammarstr T.Kotenyova, P.Nilsson-Ehle, P.Nordlund, T.Nyman, D.Ogg, C.Perss J.Sagemark, P.Stenmark, M.Sundstrom, A.G.Thorsell, S.Van Den Be J.Weigelt, L.Holmberg-Schiavone, Structural Genomics Consorti
compound source
Molecule: Atp-Dependent Rna Helicase Ddx25
Chain: A, B
Fragment: Helicase Domain: Residues 307-479
Synonym: Dead Box Protein 25, Gonadotropin-Regulated Testic Helicase;
Ec: 3.6.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddx25, Grth
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic-Bsa4
symmetry Space Group: P 43 21 2
R_factor 0.233 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.310 70.310 187.120 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CL, SO4, ZN enzyme Hydrolase E.C.3.6.1 BRENDA
note 2RB4 supersedes 2G2J
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] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (2rb4.pdb1.gz) 28 Kb
  • Biological Unit Coordinates (2rb4.pdb2.gz) 27 Kb
  • LPC: Ligand-Protein Contacts for 2RB4
  • CSU: Contacts of Structural Units for 2RB4
  • Likely Quarternary Molecular Structure file(s) for 2RB4
  • Structure Factors (179 Kb)
  • Retrieve 2RB4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2RB4 from S2C, [Save to disk]
  • Re-refined 2rb4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2RB4 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 2RB4
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2RB4, from MSDmotif at EBI
  • Fold representative 2rb4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2rb4_A] [2rb4] [2rb4_B]
  • SWISS-PROT database: [Q9UHL0]
  • Domain organization of [DDX25_HUMAN] by SWISSPFAM
  • Domain found in 2RB4: [HELICc ] by SMART
  • Other resources with information on 2RB4
  • Community annotation for 2RB4 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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