4Q0W Hydrolase Dna date Apr 02, 2014
title He Catalytic Core Of Rad2 In Complex With Dna Substrate (Com
authors M.Mietus, E.Nowak, M.Jaciuk, P.Kustosz, M.Nowotny
compound source
Molecule: Dna Repair Protein Rad2
Chain: A, B
Fragment: Rad2
Ec: 3.1.-.-
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rad2, Ygr258c
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3) Rosseta
Expression_system_vector_type: Pet

Molecule: Dna (5'- D(Tptptpgpaptpcpcpgptpcpcpapcpcptptpt)-3'
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'- D(Tptpapgpgptpgpgpapcpgpgpaptpcpaptpt)-3'
Chain: D
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.183 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
126.641 76.813 108.192 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CA, K enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding., Mietus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J, Nowotny M, Nucleic Acids Res. 2014 Aug 12. pii: gku729. PMID:25120270
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (132 Kb) [Save to disk]
  • Biological Unit Coordinates (4q0w.pdb1.gz) 125 Kb
  • LPC: Ligand-Protein Contacts for 4Q0W
  • CSU: Contacts of Structural Units for 4Q0W
  • Structure Factors (1012 Kb)
  • Retrieve 4Q0W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4Q0W from S2C, [Save to disk]
  • Re-refined 4q0w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Q0W 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 4Q0W
  • 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 4Q0W, from MSDmotif at EBI
  • Fold representative 4q0w from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4q0w_A] [4q0w] [4q0w_B] [4q0w_D] [4q0w_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4Q0W: [HhH2] [XPGI] [XPGN ] by SMART
  • Other resources with information on 4Q0W
  • Community annotation for 4Q0W at PDBWiki (http://pdbwiki.org)

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