1J2B	Transferase Rna	date	Dec 29, 2002
title	Crystal Structure Of Archaeosine Trna-Guanine Transglycosyla Complexed With Lambda-Form Trna(Val)
authors	R.Ishitani, O.Nureki, N.Nameki, N.Okada, S.Nishimura, S.Yokoyama, Structural Genomicsproteomics Initiative (Rsgi)
compound		source
Molecule: Trna(Val) Chain: C, D Engineered: Yes		Synthetic: Yes Other_details: Synthetic Trna Transcript; Sequence From Pyr Horikoshii;
Molecule: Archaeosine Trna-Guanine Transglycosylase Chain: A, B Ec: 2.4.2.29 Engineered: Yes		Organism_scientific: Pyrococcus Horikoshii Organism_taxid: 53953 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet3a
symmetry	Space Group: H 3 2	R_factor 0.225 R_Free 0.288
crystal cell	length a length b length c angle alpha angle beta angle gamma 230.834 230.834 269.255 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	3.30 Å
ligand	MG, ZN	enzyme	Transferase E.C.2.4.2.29 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme., Ishitani R, Nureki O, Nameki N, Okada N, Nishimura S, Yokoyama S, Cell 2003 May 2;113(3):383-94. PMID:12732145

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (256 Kb) [Save to disk] Biological Unit Coordinates (1j2b.pdb1.gz) 250 Kb LPC: Ligand-Protein Contacts for 1J2B CSU: Contacts of Structural Units for 1J2B Likely Quarternary Molecular Structure file(s) for 1J2B Structure Factors (553 Kb) Retrieve 1J2B in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1J2B from S2C, [Save to disk] Re-refined 1j2b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1J2B 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 1J2B

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 1J2B, from MSDmotif at EBI Structure summary from SCOR (Structural Classification of RNA) Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1j2ba3, region A:361-505 [Jmol] [rasmolscript] [script source]     - Domain d1j2ba1, region A:506-582 [Jmol] [rasmolscript] [script source]     - Domain d1j2ba2, region A:7-360 [Jmol] [rasmolscript] [script source]     - Domain d1j2bb3, region B:361-505 [Jmol] [rasmolscript] [script source]     - Domain d1j2bb1, region B:506-582 [Jmol] [rasmolscript] [script source]     - Domain d1j2bb2, region B:7-360 [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1j2b_C] [1j2b_A] [1j2b] [1j2b_B] [1j2b_D] SWISS-PROT database: [O58843] Domain organization of [ATGT_PYRHO] by SWISSPFAM Domain found in 1J2B: [PUA ] by SMART

Other resources with information on 1J2B

Community annotation for 1J2B at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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