2YVH Transcription Dna date Apr 12, 2007
title Crystal Structure Of The Operator-Binding Form Of The Multi- Binding Transcriptional Repressor Cgmr
authors H.Itou, Y.Shirakihara, I.Tanaka
compound source
Molecule: Transcriptional Regulator
Chain: A, B, C, D
Synonym: Bacterial Regulatory Protein, Tetr Family
Engineered: Yes
Organism_scientific: Corynebacterium Glutamicum
Organism_taxid: 196627
Strain: Atcc13032
Gene: Cgl2612
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b

Molecule: 5'-D(Dtpdapdapdcpdtpdgpdtpdapdcpdcpdgp C)-3';
Chain: E, G
Engineered: Yes
Other_details: Cgl2612 Operator Dna Upper Strand

Synthetic: Yes
Other_details: Sequence Found In The C.Glutamicum Genome.

Molecule: 5'-D(Dgpdgpdtpdcpdgpdgpdtpdapdcpdapdgp A)-3';
Chain: F, H
Engineered: Yes
Other_details: Cgl2612 Operator Dna Lower Strand

Synthetic: Yes
Other_details: Sequence Found In The C.Glutamicum Genome.
symmetry Space Group: P 1
R_factor 0.220 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.011 80.095 87.056 108.98 102.25 96.14
method X-Ray Diffractionresolution 2.50 Å
ligand MSE enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCrystal structures of the multidrug binding repressor Corynebacterium glutamicum CgmR in complex with inducers and with operator., Itou H, Watanabe N, Yao M, Shirakihara Y, Tanaka I, J Mol Biol. 2010 Aug 4. PMID:20691702
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (2yvh.pdb1.gz) 135 Kb
  • LPC: Ligand-Protein Contacts for 2YVH
  • CSU: Contacts of Structural Units for 2YVH
  • Likely Quarternary Molecular Structure file(s) for 2YVH
  • Structure Factors (476 Kb)
  • Retrieve 2YVH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YVH from S2C, [Save to disk]
  • Re-refined 2yvh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YVH 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 2YVH
  • 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 2YVH, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yvh_F] [2yvh_D] [2yvh_A] [2yvh_G] [2yvh_C] [2yvh] [2yvh_E] [2yvh_H] [2yvh_B]
  • SWISS-PROT database: [Q8NMG3]
  • Domain organization of [Q8NMG3_CORGL] by SWISSPFAM
  • Other resources with information on 2YVH
  • Community annotation for 2YVH 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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