1BDV Gene Regulation Dna date May 11, 1998
title Arc Fv10 Cocrystal
authors J.F.Schildbach, A.W.Karzai, B.E.Raumann, R.T.Sauer
compound source
Molecule: Dna (5'- D(Tpaptpapgptpapgpapgptpgpcptptpcptpaptp 3');
Chain: E
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'- D(Apaptpgpaptpapgpapapgpcpapcptpcptpapcp 3');
Chain: F
Engineered: Yes

Synthetic: Yes

Molecule: Protein (Arc Fv10 Repressor)
Chain: A, B, C, D
Engineered: Yes
Mutation: Yes

Organism_scientific: Enterobacteria Phage P22
Organism_taxid: 10754
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: P 1 21 1
R_factor 0.244 R_Free 0.301
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.840 56.310 52.980 90.00 105.03 90.00
method X-Ray Diffractionresolution 2.80 Å
related structures by homologous chain: 1PAR, 1QTG
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceOrigins of DNA-binding specificity: role of protein contacts with the DNA backbone., Schildbach JF, Karzai AW, Raumann BE, Sauer RT, Proc Natl Acad Sci U S A 1999 Feb 2;96(3):811-7. PMID:9927650
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk]
  • Biological Unit Coordinates (1bdv.pdb1.gz) 50 Kb
  • CSU: Contacts of Structural Units for 1BDV
  • Likely Quarternary Molecular Structure file(s) for 1BDV
  • Retrieve 1BDV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BDV from S2C, [Save to disk]
  • View 1BDV 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 1BDV
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1BDV, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bdva_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1bdvb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1bdvc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1bdvd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1bdv 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: [1bdv] [1bdv_C] [1bdv_A] [1bdv_E] [1bdv_F] [1bdv_B] [1bdv_D]
  • SWISS-PROT database: [P03050]
  • Domain organization of [RARC_BPP22] by SWISSPFAM
  • Other resources with information on 1BDV
  • Community annotation for 1BDV at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science