1RYS

REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION

Structural Biology Knowledgebase: 1RYS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.221

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1RYS

Classification: TRANSFERASE / DNA

Total Structure Weight: 100684.81


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase IV A, B 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*AP*AP*GP*GP*AP*TP*TP*CP*A)-3' C, E 13 synthetic
5'-D(*TP*CP*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' D, F 18 synthetic

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

A, B ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

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

A, B, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

F SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.221
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 98.73 α = 90.00
b = 102.29 β = 90.00
c = 106.07 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-12-22
  • Released Date: 2004-02-10
  • Deposition author(s): Ling, H., Boudsocq, F., Plosky, B., Woodgate, R., Yang, W.
  • Previous versions: 1PM8

Revision History

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