1JXL

Crystal Structure of a Y-Family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide

Structural Biology Knowledgebase: 1JXL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.221

Literature

Macromolecules
Sequence Display for 1JXL

Classification: TRANSFERASE / DNA

Total Structure Weight: 49606.90


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase IV (family Y) A 352 Sulfolobus solfataricus EC#: 2.7.7.7 IUBMB
Gene Name(s): dbh dpo4 SSO2448
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3' P 12 synthetic
5'-D(*T*TP*CP*GP*AP*AP*(BRU)P*CP*CP*TP*(BRU)P*CP*CP*CP*CP*C)-3' T 16 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DG3
Query on DG3

A 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
HDRRAMINWIWTNU-NTSWFWBYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

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

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
BRU
Query on BRU
T DNA LINKING C9 H12 Br N2 O8 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.221
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 97.12 α = 90.00
b = 101.88 β = 90.00
c = 52.45 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-09-07
  • Released Date: 2001-10-05
  • Deposition author(s): Ling, H., Boudsocq, F., Woodgate, R., Yang, W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4