2P5O	Transferase Dna	date	Mar 15, 2007
title	Crystal Structure Of Rb69 Gp43 In Complex With Dna Containin Abasic Site Analog
authors	M.Hogg, S.S.Wallace, S.Doublie
compound		source
Molecule: Template Dna Chain: E, G, I, K Engineered: Yes		Synthetic: Yes Other_details: Commercially Produced
Molecule: Primer Dna Chain: F, H, J, L Engineered: Yes		Synthetic: Yes Other_details: Commercially Produced
Molecule: Dna Polymerase Chain: A, B, C, D Synonym: Gp43 Ec: 2.7.7.7 Engineered: Yes Mutation: Yes		Organism_scientific: Enterobacteria Phage Rb69 Organism_taxid: 12353 Gene: 43 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid
symmetry	Space Group: P 1 21 1	R_factor 0.245 R_Free 0.290
crystal cell	length a length b length c angle alpha angle beta angle gamma 133.018 123.209 165.616 90.00 95.82 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	3DR, MSE	enzyme	Transferase E.C.2.7.7.7 BRENDA
note	2P5O supersedes 1RV2
Gene Ontology	Chain Function Process Component A, D, C, B DNA-directed DNA polymerase ... nuclease activity exonuclease activity 3'-5' exonuclease activity
Primary reference	Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site., Hogg M, Wallace SS, Doublie S, EMBO J. 2004 Apr 7;23(7):1483-93. Epub 2004 Apr 1. PMID:15057283

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (578 Kb) [Save to disk] Biological Unit Coordinates (2p5o.pdb1.gz) 160 Kb Biological Unit Coordinates (2p5o.pdb2.gz) 145 Kb Biological Unit Coordinates (2p5o.pdb3.gz) 159 Kb Biological Unit Coordinates (2p5o.pdb4.gz) 112 Kb LPC: Ligand-Protein Contacts for 2P5O CSU: Contacts of Structural Units for 2P5O Likely Quarternary Molecular Structure file(s) for 2P5O Structure Factors (2084 Kb) Retrieve 2P5O in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2P5O from S2C, [Save to disk] Re-refined 2p5o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2P5O 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 2P5O

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 2P5O, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2p5o_D] [2p5o_E] [2p5o_J] [2p5o_L] [2p5o_K] [2p5o] [2p5o_G] [2p5o_H] [2p5o_B] [2p5o_C] [2p5o_A] [2p5o_I] [2p5o_F] SWISS-PROT database: [Q38087] Domain organization of [DPOL_BPR69] by SWISSPFAM Domain found in 2P5O: [POLBc ] by SMART

Other resources with information on 2P5O

Community annotation for 2P5O at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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