4JWN Transferase Dna date Mar 27, 2013
title Ternary Complex Of D256a Mutant Of Dna Polymerase Beta
authors V.K.Batra, L.Perera, L.Ping, D.D.Shock, W.A.Beard, L.C.Pedersen, L.G.Pedersen, S.H.Wilson
compound source
Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7
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_vector_type: Plasmid
Expression_system_plasmid: Pwl11

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

Synthetic: Yes
Other_details: Chemically Synthesized Oligonucleotide

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

Synthetic: Yes
Other_details: Chemically Synthesized Oligonucleotide

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

Synthetic: Yes
Other_details: Chemically Synthesized Oligonucleotide
symmetry Space Group: P 1 21 1
R_factor 0.177 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.430 79.520 55.340 90.00 107.23 90.00
method X-Ray Diffractionresolution 2.39 Å
ligand CL, DUP, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceAmino Acid Substitution in the Active Site of DNA Polymerase beta Explains the Energy Barrier of the Nucleotidyl Transfer Reaction., Batra VK, Perera L, Lin P, Shock DD, Beard WA, Pedersen LC, Pedersen LG, Wilson SH, J Am Chem Soc. 2013 May 29;135(21):8078-88. doi: 10.1021/ja403842j. Epub 2013 May, 16. PMID:23647366
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (4jwn.pdb1.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 4JWN
  • CSU: Contacts of Structural Units for 4JWN
  • Structure Factors (223 Kb)
  • Retrieve 4JWN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JWN from S2C, [Save to disk]
  • Re-refined 4jwn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JWN 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 4JWN
  • 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 4JWN, from MSDmotif at EBI
  • Fold representative 4jwn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jwn_D] [4jwn_P] [4jwn] [4jwn_T] [4jwn_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4JWN: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4JWN
  • Community annotation for 4JWN at PDBWiki (http://pdbwiki.org)

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