2W9B	Transferase Dna	date	Jan 22, 2009
title	Binary Complex Of Dpo4 Bound To N2,N2-Dimethyl-Deoxyguanosin Dna
authors	R.L.Eoff, H.Zhang, I.D.Kosekov, C.J.Rizzo, M.Egli, F.P.Guengerich
compound		source
Molecule: Dna Polymerase Iv Chain: A Synonym: Pol Iv, Dpo4 Ec: 2.7.7.7 Engineered: Yes Other_details: Y-Family Dna Polymerase From Sulfolobus Solf		Organism_scientific: Sulfolobus Solfataricus Organism_taxid: 273057 Strain: P2 Atcc: 35092 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_plasmid: Pet22b
Molecule: Dna Polymerase Iv Chain: B Synonym: Pol Iv, Dpo4 Ec: 2.7.7.7 Engineered: Yes Other_details: Y-Family Dna Polymerase From Sulfolobus Solf		Organism_scientific: Sulfolobus Solfataricus Organism_taxid: 273057 Strain: P2 Atcc: 35092 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_plasmid: Pet22b
Molecule: 5'-D(Gpgpgpgpgpapapgpgpap Tptpcpdoc Chain: C, D Engineered: Yes Other_details: 14 Base Primer Dna 5'-Ggg Gga Agg Att C(Doc)		Synthetic: Yes
Molecule: 5'-D(Tpcpaptpm2gpgpapaptpcpcp Tptpcpcpcpcpc)-3'; Chain: E, F Engineered: Yes Other_details: 18 Base Template Dna 5'-Tca T(M2g)G Aat Cct		Synthetic: Yes
symmetry	Space Group: P 1 21 1	R_factor 0.239 R_Free 0.251
crystal cell	length a length b length c angle alpha angle beta angle gamma 51.794 101.776 97.268 90.00 91.95 90.00
method	X-Ray Diffraction	resolution	2.28 Å
ligand	DOC, MG, O2G	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structure-Function Relationships in Miscoding by Sulfolobus solfataricus DNA Polymerase Dpo4: GUANINE N2,N2-DIMETHYL SUBSTITUTION PRODUCES INACTIVE AND MISCODING POLYMERASE COMPLEXES., Zhang H, Eoff RL, Kozekov ID, Rizzo CJ, Egli M, Guengerich FP, J Biol Chem. 2009 Jun 26;284(26):17687-99. PMID:19542237

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk] Biological Unit Coordinates (2w9b.pdb1.gz) 71 Kb Biological Unit Coordinates (2w9b.pdb2.gz) 70 Kb LPC: Ligand-Protein Contacts for 2W9B CSU: Contacts of Structural Units for 2W9B Likely Quarternary Molecular Structure file(s) for 2W9B Structure Factors (257 Kb) Retrieve 2W9B in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2W9B from S2C, [Save to disk] Re-refined 2w9b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2W9B 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 2W9B

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 2W9B, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2w9b_A] [2w9b] [2w9b_B] [2w9b_E] [2w9b_D] [2w9b_C] [2w9b_F] SWISS-PROT database: [Q97W02] Domain organization of [DPO42_SULSO] by SWISSPFAM

Other resources with information on 2W9B

Community annotation for 2W9B at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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