1LB2 Gene Regulation Dna date Apr 01, 2002
title Structure Of The E. Coli Alpha C-Terminal Domain Of Rna Polymerase In Complex With Cap And Dna
authors B.Benoff, H.Yang, C.L.Lawson, G.Parkinson, J.Liu, E.Blatter, Y.W.Ebright, H.M.Berman, R.H.Ebright
compound source
Molecule: 5'- D(Cptptptptptptpcpcptpapapapaptpgptpgpap T)-3';
Chain: K
Engineered: Yes
Synthetic: Yes

Molecule: 5'- D(Cptpapgpaptpcpapcpaptptptptpapgpgpapap Apapapapg)-3';
Chain: J
Engineered: Yes

Synthetic: Yes

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

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna-Directed Rna Polymerase Alpha Chain
Chain: B, E
Fragment: Alpha Ctd, Alpha Carboxy Terminal Domain
Synonym: Transcriptase Alpha Chain, Rna Polymerase Alpha Subunit;
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 62 2 2
R_factor 0.211 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
175.970 175.970 158.020 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.10 Å
ligand CMP BindingDB enzyme Transferase E.C.2.7.7.6 BRENDA
note 1LB2 (Molecule of the Month:pdb48)
Gene
Ontology
ChainFunctionProcessComponent
A


E, B


Primary referenceStructural basis of transcription activation: the CAP-alpha CTD-DNA complex., Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH, Science 2002 Aug 30;297(5586):1562-6. PMID:12202833
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (1lb2.pdb1.gz) 134 Kb
  • LPC: Ligand-Protein Contacts for 1LB2
  • CSU: Contacts of Structural Units for 1LB2
  • Likely Quarternary Molecular Structure file(s) for 1LB2
  • Structure Factors (267 Kb)
  • Retrieve 1LB2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LB2 from S2C, [Save to disk]
  • Re-refined 1lb2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1LB2 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 1LB2
  • 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 1LB2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1lb2a1, region A:138-209 [Jmol] [rasmolscript] [script source]
        - Domain d1lb2a2, region A:9-137 [Jmol] [rasmolscript] [script source]
        - Domain d1lb2b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1w1lb2, region B:6-273 [Jmol] [rasmolscript] [script source]
        - Domain d1lb2e_, region E [Jmol] [rasmolscript] [script source]
  • Fold representative 1lb2 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: [1lb2] [1lb2_B] [1lb2_K] [1lb2_J] [1lb2_E] [1lb2_A]
  • SWISS-PROT database: [P0ACJ8] [P0A7Z4]
  • Domain organization of [CRP_ECOLI] [RPOA_ECOLI] by SWISSPFAM
  • Domains found in 1LB2: [HTH_CRP] [cNMP ] by SMART
  • Other resources with information on 1LB2
  • Community annotation for 1LB2 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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