1PH8 Dna Binding Protein Dna date May 29, 2003
title Crystal Structure Of The Oxytricha Nova Telomere End-Binding Complexed With Noncognate Ssdna Ggggttttgcgg
authors D.L.Theobald, S.C.Schultz
compound source
Molecule: 5'-D(Gpgpgpgptptptptpgpgpgpgpt)-3'
Chain: G, H
Engineered: Yes
Other_details: Chains G And H Are A G-Quartet Linked Dna Di Terminal Single Strand Dna Sequence Of Macronuclear Telomer
Synthetic: Yes
Other_details: Synthesized

Molecule: 5'-D(Gpgpgpgptptptptpgpcpgpg)-3'
Chain: D
Engineered: Yes
Other_details: Chain D Is Single Strand Dna. 3' Terminal Si Strand Dna Sequence Of Macronuclear Telomeres, G To C Subst

Synthetic: Yes
Other_details: Synthesized

Molecule: Telomere-Binding Protein Alpha Subunit
Chain: A
Synonym: Telomere-Binding Protein 56 Kda Subunit, Tebp Alph
Engineered: Yes
Other_details: Alanine Version

Organism_scientific: Sterkiella Nova
Organism_taxid: 200597
Gene: Mac-56a And Mac-56k And Mac-56s
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pkkt7

Molecule: Telomere-Binding Protein Beta Subunit
Chain: B
Fragment: Residues 9-224
Synonym: Telomere-Binding Protein 41 Kda Subunit, Tebp Beta
Engineered: Yes
Mutation: Yes

Organism_scientific: Sterkiella Nova
Organism_taxid: 200597
Gene: Mac-41a And Mac-41s
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pkkt7
symmetry Space Group: P 61 2 2
R_factor 0.222 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.472 93.472 423.554 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.36 Å
ligand CL, NA enzyme
related structures by homologous chain: 1PA6, 1PH3
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceNucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes., Theobald DL, Schultz SC, EMBO J 2003 Aug 15;22(16):4314-24. PMID:12912928
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (1ph8.pdb1.gz) 132 Kb
  • LPC: Ligand-Protein Contacts for 1PH8
  • CSU: Contacts of Structural Units for 1PH8
  • Likely Quarternary Molecular Structure file(s) for 1PH8
  • Structure Factors (591 Kb)
  • Retrieve 1PH8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PH8 from S2C, [Save to disk]
  • Re-refined 1ph8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PH8 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 1PH8
  • 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 1PH8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ph8a2, region A:205-328 [Jmol] [rasmolscript] [script source]
        - Domain d1ph8a3, region A:329-495 [Jmol] [rasmolscript] [script source]
        - Domain d1ph8a1, region A:36-204 [Jmol] [rasmolscript] [script source]
        - Domain d1ph8b_, region B [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: [1ph8_B] [1ph8_A] [1ph8_H] [1ph8] [1ph8_D] [1ph8_G]
  • SWISS-PROT database: [P29549] [P16458]
  • Domain organization of [TEBA_OXYNO] [TEBB_OXYNO] by SWISSPFAM
  • Domain found in 1PH8: [Telo_bind ] by SMART
  • Other resources with information on 1PH8
  • Community annotation for 1PH8 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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