1PV4 Transcription Dna date Jun 26, 2003
title X-Ray Crystal Structure Of The Rho Transcription Termination Complex With Single Stranded Dna
authors E.Skordalakes, J.M.Berger
compound source
Molecule: 5'-D(Pcpc)-3'
Chain: G, H, J, K, L
Engineered: Yes
Synthetic: Yes
Other_details: Rho Transcription Termination Factor Is An E Gene In Bacteria;

Molecule: Transcription Termination Factor Rho
Chain: A, B, C, D, E, F
Fragment: Bacterial Transcription Termination
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Rho
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet24b
symmetry Space Group: C 1 2 1
R_factor 0.270 R_Free 0.296
crystal
cell
length a length b length c angle alpha angle beta angle gamma
118.556 204.327 147.370 90.00 95.86 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand MSE enzyme
related structures by homologous chain: 1PVO, 2A8V
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceStructure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading., Skordalakes E, Berger JM, Cell 2003 Jul 11;114(1):135-46. PMID:12859904
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (401 Kb) [Save to disk]
  • Biological Unit Coordinates (1pv4.pdb1.gz) 384 Kb
  • LPC: Ligand-Protein Contacts for 1PV4
  • CSU: Contacts of Structural Units for 1PV4
  • Likely Quarternary Molecular Structure file(s) for 1PV4
  • Structure Factors (566 Kb)
  • Retrieve 1PV4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PV4 from S2C, [Save to disk]
  • Re-refined 1pv4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PV4 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 1PV4
  • 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 1PV4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pv4a1, region A:1-47 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4a3, region A:129-417 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4a2, region A:48-126 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4b2, region B:129-417 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4b1, region B:51-126 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4c1, region C:1-47 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4c3, region C:129-417 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4c2, region C:48-126 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4d1, region D:1-47 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4d3, region D:129-417 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4d2, region D:48-126 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4e1, region E:1-47 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4e3, region E:129-417 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4e2, region E:48-126 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4f1, region F:1-47 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4f3, region F:129-417 [Jmol] [rasmolscript] [script source]
        - Domain d1pv4f2, region F:48-126 [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: [1pv4_C] [1pv4] [1pv4_B] [1pv4_A] [1pv4_K] [1pv4_E] [1pv4_J] [1pv4_D] [1pv4_H] [1pv4_L] [1pv4_G] [1pv4_F]
  • SWISS-PROT database: [P0AG30]
  • Domain organization of [RHO_ECOLI] by SWISSPFAM
  • Domains found in 1PV4: [AAA] [CSP] [Rho_N ] by SMART
  • Other resources with information on 1PV4
  • Community annotation for 1PV4 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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