3M9M Transferase Dna date Mar 22, 2010
title Crystal Structure Of Dpo4 In Complex With Dna Containing The Cisplatin Lesion
authors J.H.Y.Wong, H.Ling
compound source
Molecule: Dna Polymerase Iv
Chain: B
Synonym: Pol Iv
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 2287
Strain: P2
Gene: Dbh, Dpo4, Sso2448
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: Dna (5'-D(Gpgpgpgpgpapapgpgpapapapg)
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna Oligo

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

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.285 R_Free 0.309
length a length b length c angle alpha angle beta angle gamma
98.576 101.193 52.418 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand CA, CPT, CTP, GOL enzyme Transferase E.C. BRENDA

Primary referenceStructural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4., Wong JH, Brown JA, Suo Z, Blum P, Nohmi T, Ling H, EMBO J. 2010 May 28. PMID:20512114
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (3m9m.pdb1.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 3M9M
  • CSU: Contacts of Structural Units for 3M9M
  • Structure Factors (170 Kb)
  • Retrieve 3M9M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3M9M from S2C, [Save to disk]
  • Re-refined 3m9m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3M9M 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 3M9M
  • 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 3M9M, from MSDmotif at EBI
  • Fold representative 3m9m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3m9m_P] [3m9m] [3m9m_B] [3m9m_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3M9M
  • Community annotation for 3M9M at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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