1RVC 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 Product Dna At 2 Angstroms Resolution
authors D.Kostrewa, F.K.Winkler
compound source
Molecule: Dna (5'-D(Apapapgpapt)-3')
Chain: C, E
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'-D(Aptpcptpt)-3')
Chain: D, F
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 0.156 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.290 50.340 63.880 96.66 108.76 108.41
method X-Ray Diffractionresolution 2.10 Å
ligand MG enzyme Hydrolase E.C.3.1.21.4 BRENDA
note 1RVC (Molecule of the Month:pdb8)
related structures by homologous chain: 1B95, 1RVB
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] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (1rvc.pdb1.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 1RVC
  • CSU: Contacts of Structural Units for 1RVC
  • Likely Quarternary Molecular Structure file(s) for 1RVC
  • Structure Factors (248 Kb)
  • Retrieve 1RVC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RVC from S2C, [Save to disk]
  • Re-refined 1rvc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RVC 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 1RVC
  • 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 1RVC, from MSDmotif at EBI
  • Genome occurence of 1RVC's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rvca_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1rvcb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1rvc 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: [1rvc_D] [1rvc_F] [1rvc_E] [1rvc_A] [1rvc_C] [1rvc] [1rvc_B]
  • SWISS-PROT database: [P04390]
  • Domain organization of [T2E5_ECOLX] by SWISSPFAM
  • Other resources with information on 1RVC
  • Community annotation for 1RVC 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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