1X9M Transferase Electron Transport Dna date Aug 23, 2004
title T7 Dna Polymerase In Complex With An N-2- Acetylaminofluorene-Adducted Dna
authors S.Dutta, Y.Li, D.Johnson, L.Dzantiev, C.C.Richardson, L.J.Romano, T.Ellenberger
compound source
Molecule: 5'- D(Gpgpapgpapgptpgpaptptpgpgptpapgptpgptp Gpap(2dt))-3';
Chain: C
Engineered: Yes
Other_details: Dna Primer
Synthetic: Yes

Molecule: 5'-D(Cpcpcp(8fg) Paptpcpapcpapcptpapcpcpapaptpcpapcptpcp Tpcpc)-3';
Chain: D
Engineered: Yes
Other_details: Dna Template

Synthetic: Yes

Molecule: Dna Polymerase
Chain: A
Synonym: T7 Dna Polymerase
Engineered: Yes
Mutation: Yes

Organism_scientific: Enterobacteria Phage T7
Organism_taxid: 10760
Gene: 5
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Thioredoxin 1
Chain: B
Synonym: Trx1, Trx
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Trxa, Tsnc, Fipa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.213 R_Free 0.236
length a length b length c angle alpha angle beta angle gamma
105.109 212.308 52.070 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 2DT, 8FG, MG enzyme Transferase E.C. BRENDA
related structures by homologous chain: 1TK5, 1TXX, 2TIR
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity

  • B
  • DNA polymerase processivity ...

  • Primary referenceCrystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis., Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC, Romano LJ, Ellenberger T, Proc Natl Acad Sci U S A 2004 Nov 16;101(46):16186-91. Epub . PMID:15528277
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (144 Kb) [Save to disk]
  • Biological Unit Coordinates (1x9m.pdb1.gz) 139 Kb
  • LPC: Ligand-Protein Contacts for 1X9M
  • CSU: Contacts of Structural Units for 1X9M
  • Likely Quarternary Molecular Structure file(s) for 1X9M
  • Structure Factors (556 Kb)
  • Retrieve 1X9M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1X9M from S2C, [Save to disk]
  • Re-refined 1x9m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1X9M 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 1X9M
  • 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 1X9M, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1x9ma1, region A:1-210 [Jmol] [rasmolscript] [script source]
        - Domain d1x9ma2, region A:211-704 [Jmol] [rasmolscript] [script source]
        - Domain d1x9mb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1x9m 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: [1x9m_C] [1x9m_B] [1x9m_D] [1x9m] [1x9m_A]
  • SWISS-PROT database: [P00581] [P0AA25]
  • Domain organization of [DPOL_BPT7] [THIO_ECOLI] by SWISSPFAM
  • Domain found in 1X9M: [POLAc ] by SMART
  • Other resources with information on 1X9M
  • Community annotation for 1X9M 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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