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 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_vector_type: Plasmid Expression_system_plasmid: Pet22b
symmetry	Space Group: P 21 21 21	R_factor 0.221 R_Free 0.256
crystal cell	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 Diffraction	resolution	2.03 Å
ligand	ATP, CA, EDO, NA	enzyme	Transferase E.C.2.7.7.7 BRENDA
note	1RYS (Molecule of the Month:pdb91)supersedes 1PM8
related structures	by homologous chain: 1S10, 1S9F
Gene Ontology	Chain Function Process Component A, B
Primary reference	Replication 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] (156 Kb) [Save to disk] Biological Unit Coordinates (1rys.pdb1.gz) 76 Kb Biological Unit Coordinates (1rys.pdb2.gz) 77 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

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 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] 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)

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