2VA3	Transferase	date	Aug 28, 2007
title	Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna Du Containing A Hydrophobic Thymine Isostere 2,4-Difluorotolue Nucleotide In The Template Strand
authors	A.Irimia, P.S.Pallan, M.Egli
compound		source
Molecule: Dna Polymerase Iv Chain: A Synonym: Pol Iv Ec: 2.7.7.7 Engineered: Yes Other_details: Dpo4		Organism_scientific: Sulfolobus Solfataricus Organism_taxid: 273057 Strain: P2 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet22b-Dpo4-Nhis
Molecule: 5'-D(Gpgpgpgpgpapapgpgpap Cptpa)-3' Chain: P Engineered: Yes Other_details: 13-Mer Primer		Synthetic: Yes
Molecule: 5'-D(Tptpcpapdftptpapgptpcpcp Tptpcpcpcpcpc)-3'; Chain: T Engineered: Yes Other_details: 18-Mer Template		Synthetic: Yes
symmetry	Space Group: P 21 21 2	R_factor 0.231 R_Free 0.282
crystal cell	length a length b length c angle alpha angle beta angle gamma 94.620 103.566 52.645 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.98 Å
ligand	CA, DFT, DGT	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Structure and Activity of Y-class DNA Polymerase DPO4 from Sulfolobus solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4-Difluorotoluene., Irimia A, Eoff RL, Pallan PS, Guengerich FP, Egli M, J Biol Chem. 2007 Dec 14;282(50):36421-33. Epub 2007 Oct 18. PMID:17951245

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk] Biological Unit Coordinates (2va3.pdb1.gz) 69 Kb LPC: Ligand-Protein Contacts for 2VA3 CSU: Contacts of Structural Units for 2VA3 Likely Quarternary Molecular Structure file(s) for 2VA3 Structure Factors (77 Kb) Retrieve 2VA3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VA3 from S2C, [Save to disk] Re-refined 2va3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VA3 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 2VA3

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 2VA3, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1a2va3, region A:116-236 [Jmol] [rasmolscript] [script source]     - Domain d1m2va3, region A:120-390 [Jmol] [rasmolscript] [script source]     - Domain d1q2va3, region A:146-216,A:370-405 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2va3_P] [2va3] [2va3_T] [2va3_A] SWISS-PROT database: [Q97W02] Domain organization of [DPO42_SULSO] by SWISSPFAM

Other resources with information on 2VA3

Community annotation for 2VA3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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