1VFG	Transferase Rna	date	Apr 13, 2004
title	Crystal Structure Of Trna Nucleotidyltransferase Complexed W Primer Trna And An Incoming Atp Analog
authors	K.Tomita, S.Fukai, R.Ishitani, T.Ueda, N.Takeuchi, D.G.Vassylyev, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound		source
Molecule: Rna (75-Mer) Chain: C, D Engineered: Yes		Synthetic: Yes Other_details: Rna Was Prepared By In Vitro Transcription W Rna Polymerase In Thermotoga Maritima;
Molecule: Poly A Polymerase Chain: A, B Fragment: Residues 1-390 Synonym: A-Adding Enzyme Ec: 2.7.7.19 Engineered: Yes		Organism_scientific: Aquifex Aeolicus Organism_taxid: 63363 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet
symmetry	Space Group: P 1 2 1	R_factor 0.230 R_Free 0.287
crystal cell	length a length b length c angle alpha angle beta angle gamma 109.476 125.900 58.920 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	APC	enzyme	Transferase E.C.2.7.7.19 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structural basis for template-independent RNA polymerization., Tomita K, Fukai S, Ishitani R, Ueda T, Takeuchi N, Vassylyev DG, Nureki O, Nature. 2004 Aug 5;430(7000):700-4. PMID:15295603

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk] Biological Unit Coordinates (1vfg.pdb1.gz) 72 Kb Biological Unit Coordinates (1vfg.pdb2.gz) 75 Kb LPC: Ligand-Protein Contacts for 1VFG CSU: Contacts of Structural Units for 1VFG Likely Quarternary Molecular Structure file(s) for 1VFG Structure Factors (220 Kb) Retrieve 1VFG in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1VFG from S2C, [Save to disk] Re-refined 1vfg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1VFG 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 1VFG

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1VFG, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1vfga2, region A:1-136 [Jmol] [rasmolscript] [script source]     - Domain d1vfga1, region A:137-351 [Jmol] [rasmolscript] [script source]     - Domain d1vfgb2, region B:1-136 [Jmol] [rasmolscript] [script source]     - Domain d1vfgb1, region B:137-351 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1vfg] [1vfg_A] [1vfg_C] [1vfg_B] [1vfg_D] SWISS-PROT database: [O66728] Domain organization of [O66728_AQUAE] by SWISSPFAM

Other resources with information on 1VFG

Community annotation for 1VFG at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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