1RYS Transferase Dna date Dec 22, 2003
title Replication Of A Cis-Syn Thymine Dimer At Atomic Resolution
authors H.Ling, F.Boudsocq, B.Plosky, R.Woodgate, W.Yang
compound source
Molecule: 5'-D(Gpgpgpgpapapgpgpaptptpcpa)-3'
Chain: C, E
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Tpcptptptpgpapaptpcpcptptpcpc -3';
Chain: D, F
Engineered: Yes

Synthetic: Yes

Molecule: Dna Polymerase Iv
Chain: A, B
Synonym: Pol Iv
Engineered: Yes

Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 2287
Gene: Dpo4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 21 21 21
R_factor 0.221 R_Free 0.256
length a length b length c angle alpha angle beta angle gamma
98.732 102.290 106.069 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.03 Å
ligand ATP, CA, EDO, NA enzyme Transferase E.C. BRENDA
note 1RYS (Molecule of the Month:pdb91)supersedes 1PM8
related structures by homologous chain: 1S10, 1S9F
A, B

Primary referenceReplication of a cis-syn thymine dimer at atomic resolution., Ling H, Boudsocq F, Plosky BS, Woodgate R, Yang W, Nature 2003 Aug 28;424(6952):1083-7. Epub 2003 Aug 6. PMID:12904819
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (159 Kb) [Save to disk]
  • Biological Unit Coordinates (1rys.pdb1.gz) 77 Kb
  • Biological Unit Coordinates (1rys.pdb2.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 1RYS
  • CSU: Contacts of Structural Units for 1RYS
  • Likely Quarternary Molecular Structure file(s) for 1RYS
  • Structure Factors (708 Kb)
  • Retrieve 1RYS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RYS from S2C, [Save to disk]
  • Re-refined 1rys structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RYS 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 1RYS
  • 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 1RYS, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rysa2, region A:1-240 [Jmol] [rasmolscript] [script source]
        - Domain d1rysa1, region A:241-341 [Jmol] [rasmolscript] [script source]
        - Domain d1rysb2, region B:1-240 [Jmol] [rasmolscript] [script source]
        - Domain d1rysb1, region B:241-341 [Jmol] [rasmolscript] [script source]
  • Fold representative 1rys 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: [1rys_C] [1rys_E] [1rys] [1rys_D] [1rys_B] [1rys_A] [1rys_F]
  • SWISS-PROT database: [Q97W02]
  • Domain organization of [DPO42_SULSO] by SWISSPFAM
  • Other resources with information on 1RYS
  • Community annotation for 1RYS 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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