4FLZ Transferase Dna date Jun 15, 2012
title Pyrococcus Abyssi B Family Dna Polymerase Bound To A Dsdna, Mode
authors J.Gouge, M.Delarue
compound source
Molecule: Dna Polymerase 1
Chain: A
Synonym: Pab Polymerase
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Pyrococcus Abyssi
Organism_taxid: 272844
Strain: Ge5 Orsay
Gene: Poli, Pol, Pyrab17200, Pab1128
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Primer Strand
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Chemical Synthesis

Molecule: Template Strand
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Chemical Synthesis
symmetry Space Group: P 21 21 21
R_factor 0.175 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.050 115.150 128.520 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand GOL, MG enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...


  • Primary referenceMolecular Recognition of Canonical and Deaminated Bases by P. abyssi Family B DNA Polymerase., Gouge J, Ralec C, Henneke G, Delarue M, J Mol Biol. 2012 Oct 26;423(3):315-36. doi: 10.1016/j.jmb.2012.07.025. Epub 2012 , Aug 16. PMID:22902479
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (282 Kb) [Save to disk]
  • Biological Unit Coordinates (4flz.pdb1.gz) 275 Kb
  • LPC: Ligand-Protein Contacts for 4FLZ
  • CSU: Contacts of Structural Units for 4FLZ
  • Structure Factors (646 Kb)
  • Retrieve 4FLZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4FLZ from S2C, [Save to disk]
  • Re-refined 4flz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4FLZ 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 4FLZ
  • 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 4FLZ, from MSDmotif at EBI
  • Fold representative 4flz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4flz_T] [4flz_A] [4flz_P] [4flz]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4FLZ: [POLBc ] by SMART
  • Other resources with information on 4FLZ
  • Community annotation for 4FLZ at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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