1RVA Hydrolase Dna date Oct 21, 1994
title Mg2+ Binding To The Active Site Of Eco Rv Endonuclease: A Crystallographic Study Of Complexes With Substrate And Prod Angstroms Resolution
authors D.Kostrewa, F.K.Winkler
compound source
Molecule: Dna (5'-D(Apapapgpaptpaptpcptpt)-3')
Chain: C, D
Engineered: Yes
 Synthetic: Yes

Molecule: Protein (Eco Rv (E.C.3.1.21.4))
Chain: A, B
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.162 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.440 50.150 63.950 96.54 109.05 108.11
method X-Ray Diffractionresolution 2.00 Å
ligand
enzyme Hydrolase E.C.3.1.21.4 BRENDA
note 1RVA (Molecule of the Month:pdb8)
related structures by homologous chain: 1B97, 1BSU
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity


    • Primary referenceMg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution., Kostrewa D, Winkler FK, Biochemistry 1995 Jan 17;34(2):683-96. PMID:7819264
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (97 Kb) [Save to disk]
  • Biological Unit Coordinates (1rva.pdb1.gz) 94 Kb
  • CSU: Contacts of Structural Units for 1RVA
  • Likely Quarternary Molecular Structure file(s) for 1RVA
  • Structure Factors (309 Kb)
  • Retrieve 1RVA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RVA from S2C, [Save to disk]
  • Re-refined 1rva structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1RVA 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 1RVA
  • 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 1RVA, from MSDmotif at EBI
  • Genome occurence of 1RVA's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rvaa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1rvab_, 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: [1rva] [1rva_C] [1rva_D] [1rva_A] [1rva_B]
  • SWISS-PROT database: [P04390]
  • Domain organization of [T2E5_ECOLX] by SWISSPFAM
    • Other resources with information on 1RVA
  • Community annotation for 1RVA 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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