2P5L Transcription Repressor date Mar 15, 2007
title Crystal Structure Of A Dimer Of N-Terminal Domains Of Ahrc I With An 18bp Dna Operator Site
authors J.A.Garnett, F.Marincs, S.Baumberg, P.G.Stockley, S.E.V.Phillips
compound source
Molecule: Dna (5'- D(Dcpdapdtpdgpdapdapdtpdapdapdapdapdapdtpdtp Pdg)-3');
Chain: A, E
Engineered: Yes
Synthetic: Yes
Other_details: Synthesized By Mwg-Biotech

Molecule: Dna (5'- D(Dcpdtpdtpdgpdapdapdtpdtpdtpdtpdtpdapdtpdtp Pdg)-3');
Chain: B, F
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized By Mwg-Biotech

Molecule: Arginine Repressor
Chain: C, D, G, H
Fragment: N-Terminal Domain
Synonym: Arginine Hydroxamate Resistance Protein
Engineered: Yes

Organism_scientific: Bacillus Subtilis
Organism_taxid: 1423
Gene: Argr, Ahrc
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: I 21 21 21
R_factor 0.207 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
139.105 118.770 121.230 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.85 Å
ligand SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
H, D, C, G


Primary referenceStructure and function of the arginine repressor-operator complex from Bacillus subtilis., Garnett JA, Marincs F, Baumberg S, Stockley PG, Phillips SE, J Mol Biol. 2008 May 30;379(2):284-98. Epub 2008 Mar 12. PMID:18455186
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (2p5l.pdb1.gz) 36 Kb
  • Biological Unit Coordinates (2p5l.pdb2.gz) 36 Kb
  • LPC: Ligand-Protein Contacts for 2P5L
  • CSU: Contacts of Structural Units for 2P5L
  • Likely Quarternary Molecular Structure file(s) for 2P5L
  • Structure Factors (367 Kb)
  • Retrieve 2P5L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2P5L from S2C, [Save to disk]
  • Re-refined 2p5l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2P5L 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 2P5L
  • 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 2P5L, from MSDmotif at EBI
  • Fold representative 2p5l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2p5l_D] [2p5l_G] [2p5l] [2p5l_A] [2p5l_H] [2p5l_B] [2p5l_F] [2p5l_C] [2p5l_E]
  • SWISS-PROT database: [P17893]
  • Domain organization of [ARGR_BACSU] by SWISSPFAM
  • Other resources with information on 2P5L
  • Community annotation for 2P5L 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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