1YO5 Transcription Dna date Jan 26, 2005
title Analysis Of The 2.0a Crystal Structure Of The Protein-Dna Complex Of Human Pdef Ets Domain Bound To The Prostate Specific Antigen Regulatory Site
authors Y.Wang, L.Feng, M.Said, S.Balderman, Z.Fayazi, Y.Liu, D.Ghosh, A.M.Gulick
compound source
Molecule: Enhancer Site Of Prostate Specific Antigen Promoter Region;
Chain: A
Fragment: Sense Strand Of E Site
Engineered: Yes
Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Humans. Dna Substrate For Protein Is Synthesized Chemically And Purified Through Chromatography;

Molecule: Enhancer Site Of Prostate Specific Antigen Promoter Region;
Chain: B
Fragment: Antisense Strand Of E Site
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Humans. Dna Substrate For Protein Is Synthesized Chemically And Purified Through Chromatography;

Molecule: Sam Pointed Domain Containing Ets Transcription Factor;
Chain: C
Fragment: Pdef C-Terminal Ets Domain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pdef
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (Lambda De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Gst-T-A
symmetry Space Group: P 1 21 1
R_factor 0.203 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
36.160 71.476 39.136 90.00 113.45 90.00
method X-Ray Diffractionresolution 2.00 Å
Gene
Ontology
ChainFunctionProcessComponent
C


Primary referenceAnalysis of the 2.0 A Crystal Structure of the Protein-DNA Complex of the Human PDEF Ets Domain Bound to the Prostate Specific Antigen Regulatory Site(,)., Wang Y, Feng L, Said M, Balderman S, Fayazi Z, Liu Y, Ghosh D, Gulick AM, Biochemistry 2005 May 17;44(19):7095-106. PMID:15882048
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (1yo5.pdb1.gz) 29 Kb
  • CSU: Contacts of Structural Units for 1YO5
  • Likely Quarternary Molecular Structure file(s) for 1YO5
  • Structure Factors (81 Kb)
  • Retrieve 1YO5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YO5 from S2C, [Save to disk]
  • Re-refined 1yo5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YO5 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 1YO5
  • 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 1YO5, from MSDmotif at EBI
  • Fold representative 1yo5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yo5_B] [1yo5_A] [1yo5_C] [1yo5]
  • SWISS-PROT database: [O95238]
  • Domain organization of [SPDEF_HUMAN] by SWISSPFAM
  • Domain found in 1YO5: [ETS ] by SMART
  • Other resources with information on 1YO5
  • Community annotation for 1YO5 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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