1VEQ Dna Binding Protein date Apr 03, 2004
title Mycobacterium Smegmatis Dps Hexagonal 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, G, H, I, J, K, L
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 63
R_factor 0.202 R_Free 0.248
length a length b length c angle alpha angle beta angle gamma
194.667 194.667 120.612 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.98 Å
ligand FE enzyme
F, A, J, K, E, B, H, C, D, I, G, L

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] (285 Kb) [Save to disk]
  • Biological Unit Coordinates (1veq.pdb1.gz) 277 Kb
  • LPC: Ligand-Protein Contacts for 1VEQ
  • CSU: Contacts of Structural Units for 1VEQ
  • Likely Quarternary Molecular Structure file(s) for 1VEQ
  • Structure Factors (193 Kb)
  • Retrieve 1VEQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VEQ from S2C, [Save to disk]
  • Re-refined 1veq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VEQ 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 1VEQ
  • 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 1VEQ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1veqa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1veqb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1veqc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1veqd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1veqe_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1veqf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1veqg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1veqh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1veqi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1veqj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1veqk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1veql_, region L [Jmol] [rasmolscript] [script source]
  • Fold representative 1veq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1veq_D] [1veq_H] [1veq_G] [1veq_F] [1veq_J] [1veq_E] [1veq] [1veq_C] [1veq_I] [1veq_B] [1veq_L] [1veq_K] [1veq_A]
  • SWISS-PROT database: [P0C558]
  • Domain organization of [DPS_MYCSM] by SWISSPFAM
  • Other resources with information on 1VEQ
  • Community annotation for 1VEQ 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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