1XPO

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin

Structural Biology Knowledgebase: 1XPO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.306
  • R-Value Work: 0.285

Literature

Macromolecules
Sequence Display for 1XPO

Classification: TRANSCRIPTION / RNA

Total Structure Weight: 301623.16


Macromolecule Entities
Molecule Chains Length Organism Details
Rho transcription termination factor A, B, C..., D, E, FA, B, C, D, E, F 419 Escherichia coli EC#: 3.6.4 IUBMB
Gene Name(s): rho nitA psuA rnsC sbaA tsu b3783 JW3756
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3' G, H, J... , K, L, M G, H, J, K, L, M 8 synthetic ssRNA

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AGS
Query on AGS

A, B, C, D, E, F PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'- (GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE (Synonym)
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCM
Query on BCM

B, C, D, E, F BICYCLOMYCIN
C12 H18 N2 O7
WOUDXEYYJPOSNE-VKZDFBPFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, E, F MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BCM ΔG: -25.1 kJ/mol (100) BindingDB
-TΔS: -21.8 kJ/mol (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.306
  • R-Value Work: 0.285
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 211.93 α = 90.00
b = 111.37 β = 108.79
c = 161.03 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-10-09
  • Released Date: 2005-02-08
  • Deposition author(s): Skordalakes, E., Brogan, A.P., Park, B.S., Kohn, H., Berger, J.M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor