3BDN Transcription Dna date Nov 15, 2007
title Crystal Structure Of The Lambda Repressor
authors S.E.Stayrook, P.Jaru-Ampornpan, A.Hochschild, M.Lewis
compound source
Molecule: Dna (5'- D(Dapdapdtpdapdcpdcpdapdcpdtpdgpdgpdcpdgpdgp Pdtpdapdt)-3');
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'- D(Dtpdapdtpdapdtpdcpdapdcpdcpdgpdcpdcpdapdgp Pdtpdapdt)-3');
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Lambda Repressor
Chain: A, B
Synonym: Repressor Protein Ci
Engineered: Yes
Mutation: Yes

Organism_scientific: Enterobacteria Phage Lambda
Organism_taxid: 10710
Strain: Bl21 De3
Gene: Ci
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet17b
symmetry Space Group: C 2 2 2
R_factor 0.292 R_Free 0.374
length a length b length c angle alpha angle beta angle gamma
74.431 161.099 135.256 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.91 Å
A, B

Primary referenceCrystal structure of the lambda repressor and a model for pairwise cooperative operator binding., Stayrook S, Jaru-Ampornpan P, Ni J, Hochschild A, Lewis M, Nature. 2008 Apr 24;452(7190):1022-5. PMID:18432246
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (94 Kb) [Save to disk]
  • Biological Unit Coordinates (3bdn.pdb1.gz) 86 Kb
  • CSU: Contacts of Structural Units for 3BDN
  • Likely Quarternary Molecular Structure file(s) for 3BDN
  • Structure Factors (61 Kb)
  • Retrieve 3BDN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BDN from S2C, [Save to disk]
  • Re-refined 3bdn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BDN 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 3BDN
  • 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 3BDN, from MSDmotif at EBI
  • Fold representative 3bdn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bdn] [3bdn_A] [3bdn_D] [3bdn_C] [3bdn_B]
  • SWISS-PROT database: [P03034]
  • Domain organization of [RPC1_LAMBD] by SWISSPFAM
  • Domain found in 3BDN: [HTH_XRE ] by SMART
  • Other resources with information on 3BDN
  • Community annotation for 3BDN 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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