4F5Q Transferase, Lyase Dna date May 13, 2012
title Closed Ternary Complex Of R283k Dna Polymerase Beta
authors B.D.Freudenthal, W.A.Beard, S.H.Wilson
compound source
Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7, 4.2.99.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Tap56
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pwl11

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Polydeoxyribonucleotide From Idt

Molecule: Dna (5'-D(Pgpcptpgpaptpgpcpgpc)-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Polydeoxyribonucleotide From Idt

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Polydeoxyribonucleotide From Idt
symmetry Space Group: P 1 21 1
R_factor 0.214 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.139 77.629 54.953 90.00 114.20 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand 6CF, MN, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of dNTP Intermediate States during DNA Polymerase Active Site Assembly., Freudenthal BD, Beard WA, Wilson SH, Structure. 2012 Nov 7;20(11):1829-37. doi: 10.1016/j.str.2012.08.008. Epub 2012, Sep 6. PMID:22959623
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (126 Kb) [Save to disk]
  • Biological Unit Coordinates (4f5q.pdb1.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 4F5Q
  • CSU: Contacts of Structural Units for 4F5Q
  • Structure Factors (226 Kb)
  • Retrieve 4F5Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4F5Q from S2C, [Save to disk]
  • Re-refined 4f5q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4F5Q 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 4F5Q
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4F5Q, from MSDmotif at EBI
  • Fold representative 4f5q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4f5q_T] [4f5q_D] [4f5q_A] [4f5q] [4f5q_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4F5Q: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4F5Q
  • Community annotation for 4F5Q at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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