1ZRD Gene Regulation Dna date May 19, 2005
title Crystal Structures Of Cap-Dna With All Base-Pair Substitut Position 6, Cap-[6a;17t]Icap38 Dna
authors H.M.Berman, A.A.Napoli
compound source
Molecule: 5'-D(Aptptptpcpgpapapapapaptpgpapg 3';
Chain: W, Y
Engineered: Yes
 Synthetic: Yes

Molecule: 5'-D(Cptpapgpaptpcptpcpaptptptptpt Apapt)-3';
Chain: X, Z
Engineered: Yes
Synthetic: Yes

Molecule: Catabolite Gene Activator
Chain: A, B
Synonym: Camp Receptor Protein, Camp-Regulatory Protein
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Crp, Cap, Csm
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pakcrp1
symmetry Space Group: P 21 21 21
R_factor 0.224 R_Free 0.297
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.289 75.345 178.078 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CMP BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceIndirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps., Napoli AA, Lawson CL, Ebright RH, Berman HM, J Mol Biol. 2006 Mar 17;357(1):173-83. Epub 2006 Jan 3. PMID:16427082
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (1zrd.pdb1.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 1ZRD
  • CSU: Contacts of Structural Units for 1ZRD
  • Likely Quarternary Molecular Structure file(s) for 1ZRD
  • Structure Factors (149 Kb)
  • Retrieve 1ZRD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1ZRD from S2C, [Save to disk]
  • Re-refined 1zrd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1ZRD 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 1ZRD
  • 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
  • 3D motif for 1ZRD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1zrd_Y] [1zrd_X] [1zrd] [1zrd_Z] [1zrd_A] [1zrd_B] [1zrd_W]
  • SWISS-PROT database: [P0ACJ8]
  • Domain organization of [CRP_ECOLI] by SWISSPFAM
  • Domains found in 1ZRD: [HTH_CRP] [cNMP ] by SMART
    • Other resources with information on 1ZRD
  • Community annotation for 1ZRD 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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