3DXJ Transcription,Transferase date Jul 24, 2008
title Crystal Structure Of Thermus Thermophilus Rna Polymerase Hol Complex With The Antibiotic Myxopyronin
authors K.Das, E.Arnold
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha; Chain L;
Chain: A, B, K, L
Ec: 2.7.7.6
 Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: Bacterial Rna Polymerase Beta Subunit; Chain C, M
Chain: C, M
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: Bacterial Rna Polymerase Beta-Prime Subunit; Chai
Chain: D, N
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: Bacterial Rna Polymerase Omega Subunit; Chain E,
Chain: E, O
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852

Molecule: Rna Polymerase Pricipal Sigma Factor (Rpod); Chai
Chain: F, P
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus Hb8
Organism_taxid: 300852
symmetry Space Group: P 32
R_factor 0.235 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
235.090 235.090 250.880 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
ligand MG, MPD, NE6, PO4, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, K, B, L


F, P
  • bacterial sigma factor activ...


    • M, C


    N, D


    O, E


    Primary referenceThe RNA polymerase "switch region" is a target for inhibitors., Mukhopadhyay J, Das K, Ismail S, Koppstein D, Jang M, Hudson B, Sarafianos S, Tuske S, Patel J, Jansen R, Irschik H, Arnold E, Ebright RH, Cell. 2008 Oct 17;135(2):295-307. PMID:18957204
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1118 Kb) [Save to disk]
  • Biological Unit Coordinates (3dxj.pdb1.gz) 561 Kb
  • Biological Unit Coordinates (3dxj.pdb2.gz) 564 Kb
  • LPC: Ligand-Protein Contacts for 3DXJ
  • CSU: Contacts of Structural Units for 3DXJ
  • Likely Quarternary Molecular Structure file(s) for 3DXJ
  • Structure Factors (2563 Kb)
  • Retrieve 3DXJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DXJ from S2C, [Save to disk]
  • Re-refined 3dxj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3DXJ 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 3DXJ
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3DXJ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dxj_B] [3dxj_P] [3dxj_A] [3dxj_M] [3dxj_N] [3dxj_F] [3dxj_O] [3dxj_K] [3dxj_D] [3dxj] [3dxj_C] [3dxj_L] [3dxj_E]
  • SWISS-PROT database: [Q5SKW1] [Q5SHR6] [Q8RQE9] [Q8RQE8] [Q8RQE7]
  • Domain organization of [Q5SKW1_THET8] [RPOA_THET8] [RPOB_THET8] [RPOC_THET8] [RPOZ_THET8] by SWISSPFAM
  • Domains found in 3DXJ: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
    • Other resources with information on 3DXJ
  • Community annotation for 3DXJ 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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