1VEL Dna Binding Protein date Apr 01, 2004
title Mycobacterium Smegmatis Dps Tetragonal Form
authors S.Roy, S.Gupta, S.Das, K.Sekar, D.Chatterji, M.Vijayan
compound source
Molecule: Starvation-Induced Dna Protecting Protein
Chain: A, B, C, D, E, F
Synonym: Dps
Engineered: Yes
Organism_scientific: Mycobacterium Smegmatis
Organism_taxid: 1772
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Dps, Pgem-T Easy
symmetry Space Group: P 43 21 2
R_factor 0.183 R_Free 0.210
length a length b length c angle alpha angle beta angle gamma
123.643 123.643 262.328 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.99 Å
ligand CD, NA, SO4 enzyme
related structures by homologous chain: 1VEI
F, A, D, C, E, B

Primary referenceX-ray analysis of Mycobacterium smegmatis Dps and a comparative study involving other Dps and Dps-like molecules., Roy S, Gupta S, Das S, Sekar K, Chatterji D, Vijayan M, J Mol Biol 2004 Jun 18;339(5):1103-13. PMID:15178251
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (156 Kb) [Save to disk]
  • Biological Unit Coordinates (1vel.pdb1.gz) 294 Kb
  • LPC: Ligand-Protein Contacts for 1VEL
  • CSU: Contacts of Structural Units for 1VEL
  • Likely Quarternary Molecular Structure file(s) for 1VEL
  • Structure Factors (348 Kb)
  • Retrieve 1VEL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VEL from S2C, [Save to disk]
  • Re-refined 1vel structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VEL 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 1VEL
  • 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 1VEL, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vela_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1velb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1velc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1veld_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1vele_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1velf_, region F [Jmol] [rasmolscript] [script source]
  • Fold representative 1vel from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vel_C] [1vel_E] [1vel_F] [1vel_D] [1vel] [1vel_A] [1vel_B]
  • SWISS-PROT database: [P0C558]
  • Domain organization of [DPS_MYCSM] by SWISSPFAM
  • Other resources with information on 1VEL
  • Community annotation for 1VEL 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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