1P4D Hydrolase date Apr 22, 2003
title F Factor Trai Relaxase Domain
authors S.Datta, C.Larkin, J.F.Schildbach
compound source
Molecule: Trai Protein
Chain: A, B, C
Fragment: 36 Kda N-Terminal Domain Of Trai (Residues 1-330)
Synonym: Dna Helicase I, Contains: Trai Protein
Ec: 3.6.1.-
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Trai
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24a
symmetry Space Group: P 31 2 1
R_factor 0.233 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
128.219 128.219 121.184 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
ligand EDO, MG enzyme Hydrolase E.C.3.6.1 BRENDA
Primary referenceStructural insights into single-stranded DNA binding and cleavage by F factor TraI., Datta S, Larkin C, Schildbach JF, Structure (Camb) 2003 Nov;11(11):1369-79. PMID:14604527
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (1p4d.pdb1.gz) 47 Kb
  • Biological Unit Coordinates (1p4d.pdb2.gz) 47 Kb
  • Biological Unit Coordinates (1p4d.pdb3.gz) 45 Kb
  • LPC: Ligand-Protein Contacts for 1P4D
  • CSU: Contacts of Structural Units for 1P4D
  • Likely Quarternary Molecular Structure file(s) for 1P4D
  • Structure Factors (295 Kb)
  • Retrieve 1P4D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1P4D from S2C, [Save to disk]
  • Re-refined 1p4d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1P4D 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 1P4D
  • 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 1P4D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1p4da_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1p4db_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1p4dc_, region C [Jmol] [rasmolscript] [script source]
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1p4d_B] [1p4d_A] [1p4d_C] [1p4d]
  • SWISS-PROT database: [P14565]
  • Domain organization of [TRAI1_ECOLI] by SWISSPFAM
  • Other resources with information on 1P4D
  • Community annotation for 1P4D 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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