5VI8

Structure of a mycobacterium smegmatis transcription initiation complex with an upstream-fork promoter fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.240

Literature

Macromolecules
Sequence Display for 5VI8

Classification: TRANSCRIPTION

Total Structure Weight: 457774.63


Macromolecule Entities
Molecule Chains Length Organism Details
RNA polymerase-binding protein RbpA J 114 Mycobacterium smegmatis Gene Name(s): rbpA MSMEG_3858 MSMEI_3768
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit alpha A, B 350 Mycobacterium smegmatis EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoA MSMEG_1524 MSMEI_1488
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit beta C 1169 Mycobacterium smegmatis EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoB MSMEG_1367 MSMEI_1328
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit beta' D 1317 Mycobacterium smegmatis EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoC MSMEG_1368 MSMEI_1329
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit omega E 107 Mycobacterium smegmatis EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoZ MSMEG_3053 MSMEI_2977
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
RNA polymerase sigma factor SigA F 466 Mycobacterium smegmatis Gene Name(s): rpoD sigA MSMEG_2758 MSMEI_2690
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DNA-directed RNA polymerase subunit alpha T 100 Mycobacterium smegmatis EC#: 2.7.7.6 IUBMB
Fragment: C-terminal residues 251-350
Gene Name(s): rpoA MSMEG_1524 MSMEI_1488
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (31-MER) O 31 Synthetic construct
DNA (26-MER) P 26 Synthetic construct

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

C, D, F SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

C, D, F 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.240
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 133.01 α = 90.00
b = 161.63 β = 107.72
c = 139.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-04-14
  • Released Date: 2017-04-26
  • Deposition author(s): Hubin, E.A., Campbell, E.A., Darst, S.A.
  • Previous versions:

Revision History

No revisions since initial release