3LDS	Transferase Dna	date	Jan 13, 2010
title	Crystal Structure Of Rb69 Gp43 With Dna And Datp Opposite 8-
authors	M.Hogg, J.Midkiff, J.Rudnicki, L.Reha-Krantz, S.Doublie, S.S.Wall
compound		source
Molecule: Dna-Directed Dna Polymerase Chain: A Synonym: Gp43 Ec: 2.7.7.7,3.1.11.- Engineered: Yes Mutation: Yes Other_details: Gp43		Organism_scientific: Escherichia Phage Rb69 Organism_common: Bacteriophage Rb69 Organism_taxid: 12353 Gene: 43 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Dna (5'-D(Gpcpgpgpcptpgptpcpaptpapap 3'); Chain: P Engineered: Yes Other_details: Primer		Synthetic: Yes
Molecule: Dna (5'-D(Cpap(8og) Pcptptpaptpgpapcpapgpcpcpgpcpg)-3'); Chain: T Engineered: Yes Other_details: Template		Synthetic: Yes
symmetry	Space Group: P 21 21 21	R_factor 0.242 R_Free 0.295
crystal cell	length a length b length c angle alpha angle beta angle gamma 81.011 121.002 128.668 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	8OG, DDG, DTP, MN, SO4	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	Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69., Hogg M, Rudnicki J, Midkiff J, Reha-Krantz L, Doublie S, Wallace SS, Biochemistry. 2010 Mar 23;49(11):2317-25. PMID:20166748

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (336 Kb) [Save to disk] Biological Unit Coordinates (3lds.pdb1.gz) 329 Kb LPC: Ligand-Protein Contacts for 3LDS CSU: Contacts of Structural Units for 3LDS Structure Factors (376 Kb) Retrieve 3LDS in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3LDS from S2C, [Save to disk] Re-refined 3lds structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3LDS 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 3LDS

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 3LDS, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3lds] [3lds_P] [3lds_A] [3lds_T] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3LDS: [POLBc ] by SMART

Other resources with information on 3LDS

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

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