3KHR	Transferase Dna	date	Oct 30, 2009
title	Dpo4 Post-Extension Ternary Complex With The Correct C Oppos Aminofluorene-Guanine [Af]G Lesion
authors	O.Rechkoblit, L.Malinina, D.J.Patel
compound		source
Molecule: Dna Polymerase Iv Chain: A, B Synonym: Pol Iv Ec: 2.7.7.7 Engineered: Yes		Organism_scientific: Sulfolobus Solfataricus P2 Organism_taxid: 273057 Strain: P2 Dsm 1617 Jcm 11322 Gene: Dbh, Dpo4, Sso2448 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)-Ril(Stratagene) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28a
Molecule: 5'-D(Tptpgpgpaptpgpgptpapgpcp(Ddg))- Chain: D, H Engineered: Yes Other_details: Dna Primer Strand (Dideoxy-Terminated At The		Synthetic: Yes Other_details: Dna Primer Strand (Dideoxy-Terminated At The
Molecule: 5'-D(Cpctpapapcpgpcptpapcpcpaptpcp Cpc)-3'; Chain: E, J Engineered: Yes Other_details: Dna [Af]G-Modified Template Strand		Synthetic: Yes Other_details: Dna [Af]G-Modified Template Strand
symmetry	Space Group: P 1	R_factor 0.206 R_Free 0.247
crystal cell	length a length b length c angle alpha angle beta angle gamma 52.477 53.019 99.858 81.76 76.76 70.14
method	X-Ray Diffraction	resolution	2.01 Å
ligand	AF, CA, DDG, TTP	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4., Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov NE, Broyde S, Patel DJ, Nat Struct Mol Biol. 2010 Mar;17(3):379-88. Epub 2010 Feb 14. PMID:20154704

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk] Biological Unit Coordinates (3khr.pdb1.gz) 72 Kb Biological Unit Coordinates (3khr.pdb2.gz) 73 Kb LPC: Ligand-Protein Contacts for 3KHR CSU: Contacts of Structural Units for 3KHR Structure Factors (466 Kb) Retrieve 3KHR in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3KHR from S2C, [Save to disk] Re-refined 3khr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3KHR 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 3KHR

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 3D motif for 3KHR, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3khr_J] [3khr] [3khr_A] [3khr_D] [3khr_H] [3khr_E] [3khr_B] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3KHR

Community annotation for 3KHR at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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