5WM8 Transferase Dna date Jul 28, 2017
title Structure Of The 10r (+)-Cis-Bp-Dg Modified Rev1 Ternary Com
authors O.Rechkoblit, A.Kolbanovsky, H.Landes, N.E.Geacintov, A.K.Aggarw
compound source
Molecule: Dna (5'-D(Gpgpgpgptpgptpgpgptpap(Ddg)
Chain: P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Paptpcpgpcptpapcpcpapcpapcpcpcpc)-3');
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna Repair Protein Rev1
Chain: A
Synonym: Reversionless Protein 1
Ec: 2.7.7.-
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rev1, Yor346w, O6339
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus
symmetry Space Group: P 21 21 2
R_factor 0.176 R_Free 0.214
length a length b length c angle alpha angle beta angle gamma
62.551 180.358 54.586 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.92 Å
ligand BAP, DCP, DDG, EDO, GOL, MG, PEG enzyme Transferase E.C.2.7.7 BRENDA

Primary referenceMechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase., Rechkoblit O, Kolbanovskiy A, Landes H, Geacintov NE, Aggarwal AK, Nat Commun. 2017 Oct 17;8(1):965. doi: 10.1038/s41467-017-01013-5. PMID:29042535
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (5wm8.pdb1.gz) 93 Kb
  • LPC: Ligand-Protein Contacts for 5WM8
  • CSU: Contacts of Structural Units for 5WM8
  • Structure Factors (1294 Kb)
  • Retrieve 5WM8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5WM8 from S2C, [Save to disk]
  • View 5WM8 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 5WM8
  • 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
  • Fold representative 5wm8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5wm8_P] [5wm8_T] [5wm8_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5WM8
  • Community annotation for 5WM8 at PDBWiki (http://pdbwiki.org)

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