4FBU Transferase Dna date May 23, 2012
title Dpo4 Polymerase Pre-Insertion Binary Complex With The N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion
authors K.Kirouac, A.Basu, H.Ling
compound source
Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 273057
Strain: Atcc 35092 Dsm 1617 Jcm 11322 P2
Gene: Dbh, Dpo4, Sso2448
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Primer
Chain: P, D
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna

Molecule: Dna Template
Chain: T, C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna
symmetry Space Group: P 1 21 1
R_factor 0.217 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.774 181.458 52.744 90.00 109.49 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand CA, DG8 enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural Mechanism of Replication Stalling on a Bulky Amino-Polycyclic Aromatic Hydrocarbon DNA Adduct by a Y Family DNA Polymerase., Kirouac KN, Basu AK, Ling H, J Mol Biol. 2013 Jul 20. pii: S0022-2836(13)00454-3. doi:, 10.1016/j.jmb.2013.07.020. PMID:23876706
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (292 Kb) [Save to disk]
  • Biological Unit Coordinates (4fbu.pdb1.gz) 144 Kb
  • Biological Unit Coordinates (4fbu.pdb2.gz) 143 Kb
  • LPC: Ligand-Protein Contacts for 4FBU
  • CSU: Contacts of Structural Units for 4FBU
  • Structure Factors (294 Kb)
  • Retrieve 4FBU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4FBU from S2C, [Save to disk]
  • Re-refined 4fbu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4FBU 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 4FBU
  • 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 4FBU, from MSDmotif at EBI
  • Fold representative 4fbu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4fbu_D] [4fbu_T] [4fbu_C] [4fbu_A] [4fbu_B] [4fbu_P] [4fbu]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4FBU
  • Community annotation for 4FBU at PDBWiki (http://pdbwiki.org)

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