2DB3	Hydrolase Rna	date	Dec 14, 2005
title	Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa
authors	T.Sengoku, O.Nureki, A.Nakamura, S.Kobayashi, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound		source
Molecule: 5'-R(Upupupupupupupupupu)-3' Chain: E, F, G, H Engineered: Yes		Synthetic: Yes
Molecule: Atp-Dependent Rna Helicase Vasa Chain: A, B, C, D Fragment: Residues 200-623 Synonym: Vasa Protein, Antigen Mab46f11 Ec: 3.6.1.3 Engineered: Yes		Organism_scientific: Drosophila Melanogaster Organism_common: Fruit Fly Organism_taxid: 7227 Gene: Vasa Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Codon Plus Expression_system_vector_type: Plasmid Expression_system_plasmid: Pgex-6p-1
symmetry	Space Group: P 1 21 1	R_factor 0.197 R_Free 0.250
crystal cell	length a length b length c angle alpha angle beta angle gamma 71.050 142.331 130.465 90.00 90.86 90.00
method	X-Ray Diffraction	resolution	2.20 Å
ligand	ANP, MG	enzyme	Hydrolase E.C.3.6.1.3 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa., Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S, Cell. 2006 Apr 21;125(2):287-300. PMID:16630817

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (311 Kb) [Save to disk] Biological Unit Coordinates (2db3.pdb1.gz) 79 Kb Biological Unit Coordinates (2db3.pdb2.gz) 80 Kb Biological Unit Coordinates (2db3.pdb3.gz) 81 Kb Biological Unit Coordinates (2db3.pdb4.gz) 80 Kb LPC: Ligand-Protein Contacts for 2DB3 CSU: Contacts of Structural Units for 2DB3 Likely Quarternary Molecular Structure file(s) for 2DB3 Structure Factors (1006 Kb) Retrieve 2DB3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2DB3 from S2C, [Save to disk] Re-refined 2db3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2DB3 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 2DB3

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 2DB3, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1i2db3, region B:391-573 [Jmol] [rasmolscript] [script source] Fold representative 2db3 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2db3_F] [2db3_C] [2db3_E] [2db3_G] [2db3_B] [2db3_H] [2db3] [2db3_A] [2db3_D] SWISS-PROT database: [P09052] Domain organization of [VASA_DROME] by SWISSPFAM Domains found in 2DB3: [DEXDc] [HELICc ] by SMART

Other resources with information on 2DB3

Community annotation for 2DB3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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