3CQ8	Transferase Dna	date	Apr 02, 2008
title	Ternary Complex Of The L415f Mutant Rb69 Exo(-)Polymerase
authors	X.Zhong, L.C.Pedersen, T.A.Kunkel
compound		source
Molecule: Dna (5'- D(Dapdcpdapdgpdgpdtpdapdapdgpdcpdapdgpdtpdcp Pdg)-3'); Chain: T Engineered: Yes Other_details: Template Strand		Synthetic: Yes
Molecule: Dna (5'- D(Dgpdcpdgpdgpdapdcpdtpdgpdcpdtpdtpdapdcpdc)- Chain: P Engineered: Yes Other_details: Dideoxy Terminated Primer Strand		Synthetic: Yes
Molecule: Dna Polymerase Chain: A Fragment: Rb69 Polymerase Synonym: Gp43 Ec: 2.7.7.7 Engineered: Yes Mutation: Yes		Organism_scientific: Enterobacteria Phage Organism_taxid: 12353 Strain: Rb69 Gene: 43 Expression_system: Escherichia Coli Expression_system_strain: Bl21(De3)Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pcw50
symmetry	Space Group: P 21 21 21	R_factor 0.212 R_Free 0.281
crystal cell	length a length b length c angle alpha angle beta angle gamma 80.840 117.006 127.823 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	CA, GOL, NA, TTP	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A DNA-directed DNA polymerase ... nuclease activity exonuclease activity 3'-5' exonuclease activity
Primary reference	Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity., Zhong X, Pedersen LC, Kunkel TA, Nucleic Acids Res. 2008 Jul;36(12):3892-904. Epub 2008 May 24. PMID:18503083

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (175 Kb) [Save to disk] Biological Unit Coordinates (3cq8.pdb1.gz) 168 Kb LPC: Ligand-Protein Contacts for 3CQ8 CSU: Contacts of Structural Units for 3CQ8 Likely Quarternary Molecular Structure file(s) for 3CQ8 Structure Factors (607 Kb) Retrieve 3CQ8 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3CQ8 from S2C, [Save to disk] Re-refined 3cq8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3CQ8 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 3CQ8

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 3CQ8, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3cq8_T] [3cq8_P] [3cq8] [3cq8_A] SWISS-PROT database: [Q38087] Domain organization of [DPOL_BPR69] by SWISSPFAM Domain found in 3CQ8: [POLBc ] by SMART

Other resources with information on 3CQ8

Community annotation for 3CQ8 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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