3SPD Hydrolase Dna date Jul 01, 2011
title Crystal Structure Of Aprataxin Ortholog Hnt3 In Complex With
authors Y.Gong, D.Zhu, J.Ding, C.Dou, X.Ren, T.Jiang, D.Wang
compound source
Molecule: Aprataxin-Like Protein
Chain: A, B, C, D
Fragment: Unp Residues 33-232
Synonym: Hnt3 Protein, Hit Family Protein 3
Engineered: Yes
Mutation: Yes
Organism_scientific: Schizosaccharomyces Pombe
Organism_common: Fission Yeast
Organism_taxid: 284812
Strain: Atcc 38366 972
Gene: Hnt3, Spcc18.09c
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Dna (5'-D(Tpaptptpcpcpgpaptpapgptpgp 3');
Chain: E, G
Engineered: Yes
Other_details: Short Strand Of Double-Stranded Dna

Synthetic: Yes
Other_details: Dna Oligonucleotides Were Synthesized From S Sangon Biotechnology Company (Shanghai, China).;

Molecule: Dna (5'- D(Gptpcpapcptpaptpcpgpgpapaptpgpapg)-3');
Chain: F, H
Engineered: Yes
Other_details: Long Strand Of Double-Stranded Dna

Synthetic: Yes
Other_details: Dna Oligonucleotides Were Synthesized From S Sangon Biotechnology Company (Shanghai, China)
symmetry Space Group: H 3 2
R_factor 0.175 R_Free 0.211
length a length b length c angle alpha angle beta angle gamma
220.409 220.409 135.031 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.91 Å
ligand SO4, ZN enzyme
Primary referenceCrystal structures of aprataxin ortholog Hnt3 reveal the mechanism for reversal of 5'-adenylated DNA., Gong Y, Zhu D, Ding J, Dou CN, Ren X, Gu L, Jiang T, Wang DC, Nat Struct Mol Biol. 2011 Oct 9;18(11):1297-9. doi: 10.1038/nsmb.2145. PMID:21984208
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (186 Kb) [Save to disk]
  • Biological Unit Coordinates (3spd.pdb1.gz) 91 Kb
  • Biological Unit Coordinates (3spd.pdb2.gz) 91 Kb
  • LPC: Ligand-Protein Contacts for 3SPD
  • CSU: Contacts of Structural Units for 3SPD
  • Structure Factors (1590 Kb)
  • Retrieve 3SPD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SPD from S2C, [Save to disk]
  • Re-refined 3spd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SPD 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 3SPD
  • 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 3SPD, from MSDmotif at EBI
  • Fold representative 3spd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3spd_D] [3spd_H] [3spd] [3spd_E] [3spd_F] [3spd_G] [3spd_C] [3spd_B] [3spd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3SPD
  • Community annotation for 3SPD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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