4GC6 Transferase Dna date Jul 29, 2012
title Crystal Structure Of Dpo4 In Complex With N-Mc-Damp Opposite
authors R.L.Eoff, A.Ketkar, S.Banerjee, M.K.Zafar
compound source
Molecule: Dna Polymerase Iv
Chain: A
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Sulfolobus Solfataricus P2
Organism_taxid: 273057
Strain: P2
Gene: Dbh, Dpo4, Sso2448
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b(+)

Molecule: Dna (5'-D(Gpgpgpgpgpapapgpgpaptptpcp
Chain: P
Engineered: Yes
Other_details: Primer Dna

Synthetic: Yes
Other_details: Chemically Synthesized Oligonucleotide

Molecule: Dna (5'- D(Tpcpaptpgpgpapaptpcpcptptpcpcpcpcpc)-3'
Chain: T
Engineered: Yes
Other_details: Template Dna

Synthetic: Yes
Other_details: Chemically Synthesized Oligonucleotide
symmetry Space Group: P 21 21 2
R_factor 0.202 R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.641 103.357 52.491 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand 0OH, CA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDifferential furanose selection in the active sites of archaeal DNA polymerases probed by fixed-conformation nucleotide analogues., Ketkar A, Zafar MK, Marquez VE, Banerjee S, Egli M, Eoff RL, Biochemistry. 2012 Oct 11. PMID:23050956
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (4gc6.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 4GC6
  • CSU: Contacts of Structural Units for 4GC6
  • Structure Factors (141 Kb)
  • Retrieve 4GC6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GC6 from S2C, [Save to disk]
  • Re-refined 4gc6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GC6 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 4GC6
  • 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 4GC6, from MSDmotif at EBI
  • Fold representative 4gc6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gc6_A] [4gc6_P] [4gc6] [4gc6_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4GC6
  • Community annotation for 4GC6 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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