3FMT Replication Inhibitor Dna date Dec 22, 2008
title Crystal Structure Of Seqa Bound To Dna
authors Y.S.Chung, T.Brendler, S.Austin, A.Guarne
compound source
Molecule: Protein Seqa
Chain: A, B, E, F
Fragment: Seqadelta(41-59)
Engineered: Yes
Mutation: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12
Gene: B0687, Jw0674, Seqa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a

Molecule: 5'-D(Gpapgptpcpgp(6ma) Ptpcpgpgpcpgpgpgp(6ma)Ptpcpcptptpa)-3';
Chain: C, G
Engineered: Yes

Synthetic: Yes
Other_details: Methylated Oligonucleotide

Molecule: 5'-D(Tpcptpapapgpgpaptpcpcpcpgpcpc Cpgpapc)-3';
Chain: D, H
Engineered: Yes

Synthetic: Yes
Other_details: Unmethylated Oligonucleotide
symmetry Space Group: H 3
R_factor 0.218 R_Free 0.245
length a length b length c angle alpha angle beta angle gamma
121.839 121.839 279.133 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.98 Å
ligand 6MA, MPD enzyme
F, A, E, B

Primary referenceStructural insights into the cooperative binding of SeqA to a tandem GATC repeat., Chung YS, Brendler T, Austin S, Guarne A, Nucleic Acids Res. 2009 Mar 20. PMID:19304745
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (131 Kb) [Save to disk]
  • Biological Unit Coordinates (3fmt.pdb1.gz) 64 Kb
  • Biological Unit Coordinates (3fmt.pdb2.gz) 64 Kb
  • LPC: Ligand-Protein Contacts for 3FMT
  • CSU: Contacts of Structural Units for 3FMT
  • Likely Quarternary Molecular Structure file(s) for 3FMT
  • Structure Factors (281 Kb)
  • Retrieve 3FMT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FMT from S2C, [Save to disk]
  • Re-refined 3fmt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3FMT 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 3FMT
  • 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 3FMT, from MSDmotif at EBI
  • Fold representative 3fmt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fmt] [3fmt_C] [3fmt_B] [3fmt_D] [3fmt_E] [3fmt_H] [3fmt_G] [3fmt_A] [3fmt_F]
  • SWISS-PROT database: [P0AFY8]
  • Domain organization of [SEQA_ECOLI] by SWISSPFAM
  • Other resources with information on 3FMT
  • Community annotation for 3FMT 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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