4F5R Transferase, Lyase Dna date May 13, 2012
title Open And Closed Ternary Complex Of R283k Dna Polymerase Beta Dctp Analog In The Same Asymmetric Unit
authors B.D.Freudenthal, W.A.Beard, S.H.Wilson
compound source
Molecule: Dna Polymerase Beta
Chain: A, B
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, C
Engineered: Yes

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

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpc)-3')
Chain: P, G
Engineered: Yes

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

Molecule: Dna (5'-D(Cpcpgpapcpgpgpcpgpcpaptpcp 3');
Chain: T, F
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 0.210 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.028 79.446 102.090 90.00 96.96 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand 6CF, MN, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


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] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (4f5r.pdb1.gz) 73 Kb
  • Biological Unit Coordinates (4f5r.pdb2.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 4F5R
  • CSU: Contacts of Structural Units for 4F5R
  • Structure Factors (782 Kb)
  • Retrieve 4F5R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4F5R from S2C, [Save to disk]
  • Re-refined 4f5r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4F5R 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 4F5R
  • 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 4F5R, from MSDmotif at EBI
  • Fold representative 4f5r from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4f5r] [4f5r_C] [4f5r_P] [4f5r_D] [4f5r_G] [4f5r_A] [4f5r_B] [4f5r_T] [4f5r_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4F5R: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4F5R
  • Community annotation for 4F5R at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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