1S97 Transferase Dna date Feb 03, 2004
title Dpo4 With Gt Mismatch
authors J.Trincao, R.E.Johnson, W.T.Wolfle, C.R.Escalante, S.Prakash, L.Prakash, A.K.Aggarwal
compound source
Molecule: 5'-D(Gpgpgpgpgpapapgpgpapcptpg)-3'
Chain: E, F, G, H
Engineered: Yes
Synthetic: Yes

Molecule: 5'- D(Ttpcpapgptpapgptpcpcptptpcpcpcpcpc)-3';
Chain: I, J, K, L
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase Iv
Chain: A, B, C, D
Synonym: Pol Iv
Ec: 2.7.7.7
Engineered: Yes

Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 2287
Gene: Dbh, Dpo4, Sso2448
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.218 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.433 100.644 110.426 90.00 94.89 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand CA, DCT enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1N56, 1RYR
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceDpo4 is hindered in extending a G.T mismatch by a reverse wobble., Trincao J, Johnson RE, Wolfle WT, Escalante CR, Prakash S, Prakash L, Aggarwal AK, Nat Struct Mol Biol 2004 May;11(5):457-62. Epub 2004 Apr 11. PMID:15077104
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (288 Kb) [Save to disk]
  • Biological Unit Coordinates (1s97.pdb1.gz) 73 Kb
  • Biological Unit Coordinates (1s97.pdb2.gz) 74 Kb
  • Biological Unit Coordinates (1s97.pdb3.gz) 74 Kb
  • Biological Unit Coordinates (1s97.pdb4.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 1S97
  • CSU: Contacts of Structural Units for 1S97
  • Likely Quarternary Molecular Structure file(s) for 1S97
  • Structure Factors (707 Kb)
  • Retrieve 1S97 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1S97 from S2C, [Save to disk]
  • Re-refined 1s97 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1S97 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 1S97
  • 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 1S97, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1s97a2, region A:1-240 [Jmol] [rasmolscript] [script source]
        - Domain d1s97a1, region A:241-341 [Jmol] [rasmolscript] [script source]
        - Domain d1s97b2, region B:1-240 [Jmol] [rasmolscript] [script source]
        - Domain d1s97b1, region B:241-341 [Jmol] [rasmolscript] [script source]
        - Domain d1s97c2, region C:1-240 [Jmol] [rasmolscript] [script source]
        - Domain d1s97c1, region C:241-341 [Jmol] [rasmolscript] [script source]
        - Domain d1s97d2, region D:1-240 [Jmol] [rasmolscript] [script source]
        - Domain d1s97d1, region D:241-341 [Jmol] [rasmolscript] [script source]
  • Fold representative 1s97 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: [1s97_F] [1s97_G] [1s97_A] [1s97_J] [1s97_H] [1s97_B] [1s97_C] [1s97_L] [1s97_E] [1s97_I] [1s97_K] [1s97_D] [1s97]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 1S97
  • Community annotation for 1S97 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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