1XI1 Transferase Dna date Sep 21, 2004
title Phi29 Dna Polymerase Ssdna Complex, Monoclinic Crystal Form
authors S.Kamtekar, A.J.Berman, J.Wang, J.M.Lazaro, M.De Vega, L.Blanco, M T.A.Steitz
compound source
Molecule: 5'-D(Ptptptptpt)-3'
Chain: C, D
Engineered: Yes
Synthetic: Yes

Molecule: Dna Polymerase
Chain: A, B
Synonym: Early Protein Gp2
Engineered: Yes
Mutation: Yes

Organism_scientific: Bacillus Phage Phi29
Organism_taxid: 10756
Gene: 2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.243 R_Free 0.277
length a length b length c angle alpha angle beta angle gamma
60.557 170.563 68.813 90.00 106.99 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand MG enzyme Transferase E.C. BRENDA
related structures by homologous chain: 1XHX
A, B
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity

  • Primary referenceCorrection of X-ray intensities from single crystals containing lattice-translocation defects., Wang J, Kamtekar S, Berman AJ, Steitz TA, Acta Crystallogr D Biol Crystallogr. 2005 Jan;61(Pt 1):67-74. Epub 2004, Dec 17. PMID:15608377
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (202 Kb) [Save to disk]
  • Biological Unit Coordinates (1xi1.pdb1.gz) 100 Kb
  • Biological Unit Coordinates (1xi1.pdb2.gz) 100 Kb
  • LPC: Ligand-Protein Contacts for 1XI1
  • CSU: Contacts of Structural Units for 1XI1
  • Likely Quarternary Molecular Structure file(s) for 1XI1
  • Structure Factors (563 Kb)
  • Retrieve 1XI1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XI1 from S2C, [Save to disk]
  • Re-refined 1xi1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1XI1 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 1XI1
  • 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 1XI1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1xi1a2, region A:188-575 [Jmol] [rasmolscript] [script source]
        - Domain d1xi1a1, region A:5-187 [Jmol] [rasmolscript] [script source]
  • Fold representative 1xi1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1xi1] [1xi1_C] [1xi1_A] [1xi1_D] [1xi1_B]
  • SWISS-PROT database: [P03680]
  • Domain organization of [DPOL_BPPH2] by SWISSPFAM
  • Domain found in 1XI1: [POLBc ] by SMART
  • Other resources with information on 1XI1
  • Community annotation for 1XI1 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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