1DZF Transferase date Feb 25, 2000
title Rpb5 From S.Cerevisiae
authors F.Todone, R.O.J.Weinzierl, P.Brick, S.Onesti
compound source
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 1;
Chain: A
Synonym: Rna Polymerases I, II, And III Subunit Abc1, Abc27 Dna-Directed Rna Polymerases I, II, And III 27 Kda Polypep
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: S288c
Cellular_location: Nuclear
Gene: Ybr154c Or Ybr1204
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex2tk
Other_details: Synthetic Gene
symmetry Space Group: C 2 2 21
R_factor 0.217 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.050 82.220 134.810 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.9 Å
ligand
enzyme Transferase E.C.2.7.7.6 BRENDA
related structures by homologous chain: 1TWF
Gene
Ontology
ChainFunctionProcessComponent
A
  • RNA-directed 5'-3' RNA polym...


  • Primary referenceCrystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target., Todone F, Weinzierl RO, Brick P, Onesti S, Proc Natl Acad Sci U S A 2000 Jun 6;97(12):6306-10. PMID:10841537
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (43 Kb) [Save to disk]
  • Biological Unit Coordinates (1dzf.pdb1.gz) 39 Kb
  • CSU: Contacts of Structural Units for 1DZF
  • Likely Quarternary Molecular Structure file(s) for 1DZF
  • Structure Factors (139 Kb)
  • Retrieve 1DZF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DZF from S2C, [Save to disk]
  • Re-refined 1dzf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DZF 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 1DZF
  • 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 1DZF, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dzfa2, region A:144-215 [Jmol] [rasmolscript] [script source]
        - Domain d1dzfa1, region A:5-143 [Jmol] [rasmolscript] [script source]
  • Fold representative 1dzf from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1dzf] [1dzf_A]
  • SWISS-PROT database: [P20434]
  • Domain organization of [RPAB1_YEAST] by SWISSPFAM
  • Other resources with information on 1DZF
  • Community annotation for 1DZF 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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