1Q9X Transferase,Replication Dna date Aug 26, 2003
title Crystal Structure Of Enterobacteria Phage Rb69 Gp43 Dna Poly Complexed With Tetrahydrofuran Containing Dna
authors E.Freisinger, A.P.Grollman, H.Miller, C.Kisker
compound source
Molecule: 5'-Gcggactgcttac(Dideoxycytidine)-3'
Chain: E, F, G, H
Engineered: Yes
 Synthetic: Yes

Molecule: 5'-Ac(Tetrahydrofuran)Ggtaagcagtccgcgg-3'
Chain: I, J, K, L
Engineered: Yes
Synthetic: Yes

Molecule: Dna Polymerase
Chain: A, B, C, D
Synonym: Gp43
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage Rb69
Organism_taxid: 12353
Gene: 43
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: M15
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe30
symmetry Space Group: P 1 21 1
R_factor 0.215 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
131.948 122.237 165.358 90.00 96.85 90.00
method X-Ray Diffractionresolution 2.69 Å
ligand 3DR, CA, DGP, DOC enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1CLQ, 1IG9
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


    • Primary referenceLesion (in)tolerance reveals insights into DNA replication fidelity., Freisinger E, Grollman AP, Miller H, Kisker C, EMBO J 2004 Apr 7;23(7):1494-505. Epub 2004 Apr 1. PMID:15057282
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1355 Kb) [Save to disk]
  • Biological Unit Coordinates (1q9x.pdb1.gz) 345 Kb
  • Biological Unit Coordinates (1q9x.pdb2.gz) 342 Kb
  • Biological Unit Coordinates (1q9x.pdb3.gz) 339 Kb
  • Biological Unit Coordinates (1q9x.pdb4.gz) 342 Kb
  • LPC: Ligand-Protein Contacts for 1Q9X
  • CSU: Contacts of Structural Units for 1Q9X
  • Likely Quarternary Molecular Structure file(s) for 1Q9X
  • Structure Factors (961 Kb)
  • Retrieve 1Q9X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Q9X from S2C, [Save to disk]
  • Re-refined 1q9x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1Q9X 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 1Q9X
  • 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 1Q9X, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q9xa1, region A:1-375 [Jmol] [rasmolscript] [script source]
        - Domain d1q9xa2, region A:376-903 [Jmol] [rasmolscript] [script source]
        - Domain d1q9xb1, region B:1-375 [Jmol] [rasmolscript] [script source]
        - Domain d1q9xb2, region B:376-903 [Jmol] [rasmolscript] [script source]
        - Domain d1q9xc1, region C:1-375 [Jmol] [rasmolscript] [script source]
        - Domain d1q9xc2, region C:376-903 [Jmol] [rasmolscript] [script source]
        - Domain d1q9xd1, region D:1-375 [Jmol] [rasmolscript] [script source]
        - Domain d1q9xd2, region D:376-903 [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: [1q9x_B] [1q9x_H] [1q9x_L] [1q9x_K] [1q9x_J] [1q9x_D] [1q9x] [1q9x_C] [1q9x_A] [1q9x_G] [1q9x_F] [1q9x_E] [1q9x_I]
  • SWISS-PROT database: [Q38087]
  • Domain organization of [DPOL_BPR69] by SWISSPFAM
  • Domain found in 1Q9X: [POLBc ] by SMART
    • Other resources with information on 1Q9X
  • Community annotation for 1Q9X 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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