1T2T Hydrolase Dna date Apr 22, 2004
title Crystal Structure Of The Dna-Binding Domain Of Intron Endonuclease I-Tevi With Operator Site
authors D.R.Edgell, V.Derbyshire, P.Van Roey, S.Labonne, M.J.Stanger, Z.Li, T.M.Boyd, D.A.Shub, M.Belfort
compound source
Molecule: 5'- D(Tptptpgptpapgpgpapcptpgpcpcpcptptptpap Apt)-3';
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: 5'- D(Apaptptpapapapgpgpgpcpapgptpcpcptpapcp Apa)-3';
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Intron-Associated Endonuclease 1
Chain: A
Fragment: Dna-Binding Domain (Residues 130-245)
Synonym: I-Tevi, Irf Protein
Ec: 3.1.-.-
Engineered: Yes

Organism_scientific: Enterobacteria Phage T4
Organism_taxid: 10665
Gene: Itevir
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.238 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.660 64.890 42.810 90.00 90.48 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand ZN enzyme Hydrolase E.C.3.1 BRENDA
related structures by homologous chain: 1I3J
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceIntron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor., Edgell DR, Derbyshire V, Van Roey P, LaBonne S, Stanger MJ, Li Z, Boyd TM, Shub DA, Belfort M, Nat Struct Mol Biol. 2004 Oct;11(10):936-44. Epub 2004 Sep 7. PMID:15361856
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (39 Kb) [Save to disk]
  • Biological Unit Coordinates (1t2t.pdb1.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 1T2T
  • CSU: Contacts of Structural Units for 1T2T
  • Likely Quarternary Molecular Structure file(s) for 1T2T
  • Structure Factors (136 Kb)
  • Retrieve 1T2T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1T2T from S2C, [Save to disk]
  • Re-refined 1t2t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1T2T 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 1T2T
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1T2T, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1t2ta_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1t2t from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1t2t_A] [1t2t_B] [1t2t] [1t2t_C]
  • SWISS-PROT database: [P13299]
  • Domain organization of [TEV1_BPT4] by SWISSPFAM
  • Domain found in 1T2T: [IENR2 ] by SMART
  • Other resources with information on 1T2T
  • Community annotation for 1T2T at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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