2PFQ Transferase, Lyase Dna date Apr 05, 2007
title Manganese Promotes Catalysis In A Dna Polymerase Lambda-Dna
authors M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel
compound source
Molecule: Template
Chain: T
Engineered: Yes


Molecule: Primer
Chain: P
Engineered: Yes


Molecule: Downstream Primer
Chain: D
Engineered: Yes


Molecule: Dna Polymerase Lambda
Chain: A
Synonym: Pol Lambda, Dna Polymerase Kappa, Dna Polymerase B Beta2;
Ec: 2.7.7.7, 4.2.99.-
Engineered: Yes
Mutation: Yes
Synthetic: Yes


Synthetic: Yes


Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Poll
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-22b (+)
symmetry Space Group: P 21 21 21
R_factor 0.256 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.091 63.485 139.775 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand DCP, MG, MN, NA, PPV enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceRole of the catalytic metal during polymerization by DNA polymerase lambda., Garcia-Diaz M, Bebenek K, Krahn JM, Pedersen LC, Kunkel TA, DNA Repair (Amst). 2007 Apr 30;. PMID:17475573
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (2pfq.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 2PFQ
  • CSU: Contacts of Structural Units for 2PFQ
  • Likely Quarternary Molecular Structure file(s) for 2PFQ
  • Structure Factors (378 Kb)
  • Retrieve 2PFQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PFQ from S2C, [Save to disk]
  • Re-refined 2pfq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2PFQ 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 2PFQ
  • 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 2PFQ, from MSDmotif at EBI
  • Fold representative 2pfq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pfq_A] [2pfq_P] [2pfq_D] [2pfq_T] [2pfq]
  • SWISS-PROT database: [Q9UGP5]
  • Domain organization of [DPOLL_HUMAN] by SWISSPFAM
  • Domains found in 2PFQ: [HhH1] [POLXc ] by SMART
  • Other resources with information on 2PFQ
  • Community annotation for 2PFQ 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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