1JX4 Transferase Dna date Sep 05, 2001
title Crystal Structure Of A Y-Family Dna Polymerase In A Ternary With Dna Substrates And An Incoming Nucleotide
authors H.Ling, F.Boudsocq, R.Woodgate, W.Yang
compound source
Molecule: 5'-D(Gpgpgpgpgpapapgpgpapcptpa)-3'
Chain: P
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Ttpcpaptptpapgptpcpcptptpcpcp 3';
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase Iv (Family Y)
Chain: A
Ec: 2.7.7.7
Engineered: Yes

Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 2287
Gene: Dpo4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 21 21 2
R_factor 0.213 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
97.090 102.820 52.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand ADI, CA, MG, MSE enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1S9F
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication., Ling H, Boudsocq F, Woodgate R, Yang W, Cell 2001 Oct 5;107(1):91-102. PMID:11595188
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (1jx4.pdb1.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 1JX4
  • CSU: Contacts of Structural Units for 1JX4
  • Likely Quarternary Molecular Structure file(s) for 1JX4
  • Structure Factors (596 Kb)
  • Retrieve 1JX4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JX4 from S2C, [Save to disk]
  • Re-refined 1jx4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1JX4 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 1JX4
  • 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 1JX4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jx4a2, region A:1-240 [Jmol] [rasmolscript] [script source]
        - Domain d1jx4a1, region A:241-341 [Jmol] [rasmolscript] [script source]
  • Fold representative 1jx4 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: [1jx4_A] [1jx4_T] [1jx4] [1jx4_P]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 1JX4
  • Community annotation for 1JX4 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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