4ESV

A New Twist on the Translocation Mechanism of Helicases from the Structure of DnaB with its Substrates

Structural Biology Knowledgebase: 4ESV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.242

Literature

Macromolecules
Sequence Display for 4ESV

Classification: HYDROLASE / DNA

Total Structure Weight: 623326.44


Macromolecule Entities
Molecule Chains Length Organism Details
Replicative helicase A, B, C..., D, E, F, G, H, I, J, K, LA, B, C, D, E, F, G, H, I, J, K, L 454 Geobacillus stearothermophilus EC#: 3.6.4.12 IUBMB
Gene Name(s): dnaB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' V 14 synthetic
5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3' W 13 synthetic

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

A, C, D, E, F, G, I, J, K, L GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MES
Query on MES

C, E, I, W 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ALF
Query on ALF

A, C, D, E, G, I, J, K, L TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C, D, E, F, G, I, L CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.242
  • Space Group: P 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 149.12 α = 90.00
b = 180.32 β = 90.00
c = 279.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-23
  • Released Date: 2012-10-24
  • Deposition author(s): Itsathitphaisarn, O., Wing, R.A., Eliason, W.K., Wang, J., Steitz, T.A.

Revision History

No revisions since initial release