2RDJ Transferase Dna date Sep 24, 2007
title Snapshots Of A Y-Family Dna Polymerase In Replication: Dpo4 Binaryternary Complex Forms
authors J.H.Y.Wong, H.Ling
compound source
Molecule: Dna (5'- D(Dgpdgpdgpdapdcpdcpdcpdtpdtpdcpdgpdapdapdt)-
Chain: C, E
Engineered: Yes
Other_details: Dna Primer Strand
Synthetic: Yes

Molecule: Dna (5'- D(Pdtpdtpdapdtpdtpdcpdgpdapdapdgpdgpdgpdtpdcp 3');
Chain: D
Engineered: Yes
Other_details: Dna Template Strand From Polypeptide Chain A

Synthetic: Yes

Molecule: Dna (5'- D(Pdtpdapdtpdtpdcpdgpdapdapdgpdgpdgpdtpdcpdcp
Chain: F
Engineered: Yes
Other_details: Dna Template Strand From Polypeptide Chain B

Synthetic: Yes

Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Engineered: Yes

Organism_scientific: Sulfolobus Solfataricus
Strain: P2
Gene: Dbh, Dpo4
Expression_system: Escherichia Coli
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 21 21 21
R_factor 0.210 R_Free 0.256
length a length b length c angle alpha angle beta angle gamma
97.993 102.510 106.109 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand CA, GOL, TMP enzyme Transferase E.C. BRENDA
A, B

Primary referenceSnapshots of a Y-family DNA polymerase in replication: substrate-induced conformational transitions and implications for fidelity of Dpo4., Wong JH, Fiala KA, Suo Z, Ling H, J Mol Biol. 2008 May 30;379(2):317-30. Epub 2008 Mar 28. PMID:18448122
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (2rdj.pdb1.gz) 73 Kb
  • Biological Unit Coordinates (2rdj.pdb2.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 2RDJ
  • CSU: Contacts of Structural Units for 2RDJ
  • Likely Quarternary Molecular Structure file(s) for 2RDJ
  • Structure Factors (1275 Kb)
  • Retrieve 2RDJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2RDJ from S2C, [Save to disk]
  • Re-refined 2rdj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2RDJ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2RDJ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2RDJ, from MSDmotif at EBI
  • Fold representative 2rdj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2rdj_D] [2rdj_B] [2rdj] [2rdj_A] [2rdj_C] [2rdj_E] [2rdj_F]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 2RDJ
  • Community annotation for 2RDJ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science