1XPU Transcription Rna date Oct 09, 2004
title Structural Mechanism Of Inhibition Of The Rho Transcription Termination Factor By The Antibiotic 5a-(3-Formylphenylsulf Dihydrobicyclomycin (Fpdb)
authors E.Skordalakes, A.P.Brogan, B.S.Park, H.Kohn, J.M.Berger
compound source
Molecule: 5'-R(Cpupcpupcpupcpu)-3'
Chain: G, M, H, J, K, L
Engineered: Yes
Other_details: Ssrna
Synthetic: Yes

Molecule: Rho Transcription Termination Factor
Chain: A, B, C, D, E, F
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: C 1 2 1
R_factor 0.276 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
119.477 206.935 148.607 90.00 96.95 90.00
method X-Ray Diffractionresolution 3.05 Å
ligand AGS, FPD, MG BindingDB enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceStructural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin., Skordalakes E, Brogan AP, Park BS, Kohn H, Berger JM, Structure (Camb) 2005 Jan;13(1):99-109. PMID:15642265
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (364 Kb) [Save to disk]
  • Biological Unit Coordinates (1xpu.pdb1.gz) 63 Kb
  • Biological Unit Coordinates (1xpu.pdb2.gz) 64 Kb
  • Biological Unit Coordinates (1xpu.pdb3.gz) 64 Kb
  • Biological Unit Coordinates (1xpu.pdb4.gz) 64 Kb
  • Biological Unit Coordinates (1xpu.pdb5.gz) 64 Kb
  • Biological Unit Coordinates (1xpu.pdb6.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 1XPU
  • CSU: Contacts of Structural Units for 1XPU
  • Likely Quarternary Molecular Structure file(s) for 1XPU
  • Structure Factors (470 Kb)
  • Retrieve 1XPU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XPU from S2C, [Save to disk]
  • Re-refined 1xpu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1XPU 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 1XPU
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1XPU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1xpua1, region A:1-47 [Jmol] [rasmolscript] [script source]
        - Domain d1xpua3, region A:129-417 [Jmol] [rasmolscript] [script source]
        - Domain d1xpua2, region A:48-126 [Jmol] [rasmolscript] [script source]
        - Domain d1xpub1, region B:1-47 [Jmol] [rasmolscript] [script source]
        - Domain d1xpub3, region B:129-417 [Jmol] [rasmolscript] [script source]
        - Domain d1xpub2, region B:48-126 [Jmol] [rasmolscript] [script source]
        - Domain d1xpuc1, region C:1-47 [Jmol] [rasmolscript] [script source]
        - Domain d1xpuc3, region C:129-417 [Jmol] [rasmolscript] [script source]
        - Domain d1xpuc2, region C:48-126 [Jmol] [rasmolscript] [script source]
        - Domain d1xpud1, region D:1-47 [Jmol] [rasmolscript] [script source]
        - Domain d1xpud3, region D:129-417 [Jmol] [rasmolscript] [script source]
        - Domain d1xpud2, region D:48-126 [Jmol] [rasmolscript] [script source]
        - Domain d1xpue1, region E:1-47 [Jmol] [rasmolscript] [script source]
        - Domain d1xpue3, region E:129-417 [Jmol] [rasmolscript] [script source]
        - Domain d1xpue2, region E:48-126 [Jmol] [rasmolscript] [script source]
        - Domain d1xpuf1, region F:1-47 [Jmol] [rasmolscript] [script source]
        - Domain d1xpuf3, region F:129-417 [Jmol] [rasmolscript] [script source]
        - Domain d1xpuf2, region F:48-126 [Jmol] [rasmolscript] [script source]
  • 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: [1xpu_D] [1xpu_J] [1xpu_E] [1xpu_C] [1xpu_A] [1xpu_B] [1xpu_L] [1xpu_M] [1xpu_K] [1xpu] [1xpu_H] [1xpu_F] [1xpu_G]
  • SWISS-PROT database: [P0AG30]
  • Domain organization of [RHO_ECOLI] by SWISSPFAM
  • Domains found in 1XPU: [AAA] [CSP] [Rho_N ] by SMART
  • Other resources with information on 1XPU
  • Community annotation for 1XPU 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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