1O3T Gene Regulation Dna date Mar 18, 2003
title Protein-Dna Recognition And Dna Deformation Revealed In Crys Structures Of Cap-Dna Complexes
authors S.Chen, J.Vojtechovsky, G.N.Parkinson, R.H.Ebright, H.M.Berman
compound source
Molecule: 5'-D(Gpcpgpapapapapaptpgpcpgpapt)-3
Chain: C, F
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Cptpapgpaptpcpgpcpaptptptptpt 3';
Chain: D, E
Engineered: Yes

Synthetic: Yes

Molecule: Catabolite Gene Activator Protein
Chain: A, B
Synonym: Cap, Camp Receptor Protein, Camp-Regulatory Protei
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.230 R_Free 0.303
crystal
cell
length a length b length c angle alpha angle beta angle gamma
136.990 152.800 76.060 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CMP BindingDB enzyme
note 1O3T supersedes 1DBC
related structures by homologous chain: 1O3R, 1RUO
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceIndirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking., Chen S, Vojtechovsky J, Parkinson GN, Ebright RH, Berman HM, J Mol Biol 2001 Nov 16;314(1):63-74. PMID:11724532
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (96 Kb) [Save to disk]
  • Biological Unit Coordinates (1o3t.pdb1.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 1O3T
  • CSU: Contacts of Structural Units for 1O3T
  • Likely Quarternary Molecular Structure file(s) for 1O3T
  • Structure Factors (144 Kb)
  • Retrieve 1O3T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1O3T from S2C, [Save to disk]
  • Re-refined 1o3t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1O3T 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 1O3T
  • 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 1O3T, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1o3ta1, region A:138-207 [Jmol] [rasmolscript] [script source]
        - Domain d1o3ta2, region A:9-137 [Jmol] [rasmolscript] [script source]
        - Domain d1o3tb1, region B:138-205 [Jmol] [rasmolscript] [script source]
        - Domain d1o3tb2, region B:9-137 [Jmol] [rasmolscript] [script source]
  • Fold representative 1o3t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1o3t_E] [1o3t_D] [1o3t_B] [1o3t_C] [1o3t] [1o3t_A] [1o3t_F]
  • SWISS-PROT database: [P0ACJ8]
  • Domain organization of [CRP_ECOLI] by SWISSPFAM
  • Domains found in 1O3T: [HTH_CRP] [cNMP ] by SMART
  • Other resources with information on 1O3T
  • Community annotation for 1O3T 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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