3GIL	Transferase Dna	date	Mar 05, 2009
title	Dpo4 Extension Ternary Complex With Oxog(Anti)-T(Anti) Pair
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 Atcc: 35092 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(Gptptpgpgpaptpgpgptpapgp(2dt))- Chain: D, H Engineered: Yes Other_details: Primer Strand (Dideoxy-Terminated At 3'-End)		Synthetic: Yes Other_details: Dna Primer Strand
Molecule: 5'-D(Cptpapapcp(8og) Pcptpapcpcpaptpcpcpapapc)-3'; Chain: E, J Engineered: Yes Other_details: Oxog-Modified Template Strand		Synthetic: Yes Other_details: Dna Oxog-Modified Template Strand
symmetry	Space Group: P 1 21 1	R_factor 0.200 R_Free 0.259
crystal cell	length a length b length c angle alpha angle beta angle gamma 53.289 110.682 102.190 90.00 99.22 90.00
method	X-Ray Diffraction	resolution	2.71 Å
ligand	2DT, 8OG, CA, DGT	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases., Rechkoblit O, Malinina L, Cheng Y, Geacintov NE, Broyde S, Patel DJ, Structure. 2009 May 13;17(5):725-36. PMID:19446528

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk] Biological Unit Coordinates (3gil.pdb1.gz) 70 Kb Biological Unit Coordinates (3gil.pdb2.gz) 68 Kb LPC: Ligand-Protein Contacts for 3GIL CSU: Contacts of Structural Units for 3GIL Likely Quarternary Molecular Structure file(s) for 3GIL Structure Factors (229 Kb) Retrieve 3GIL in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3GIL from S2C, [Save to disk] Re-refined 3gil structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3GIL 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 3GIL

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 3GIL, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3gil_B] [3gil] [3gil_E] [3gil_J] [3gil_H] [3gil_D] [3gil_A] SWISS-PROT database: [Q97W02] Domain organization of [DPO42_SULSO] by SWISSPFAM

Other resources with information on 3GIL

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

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