1STX Hydrolase Dna date Mar 25, 2004
title Structure Of The K38a Mutant Of Ecorv Bound To Cognate Dna A
authors N.C.Horton, J.J.Perona
compound source
Molecule: 5'-D(Apapapgpapt)-3'
Chain: C, E
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Paptpcptpt)-3'
Chain: D, F
Engineered: Yes

Synthetic: Yes

Molecule: Type II Restriction Enzyme Ecorv
Chain: A, B
Synonym: Endonuclease Ecorv; R.Ecorv; Type II Site-Specific Deoxyribonuclease Ecorv;
Engineered: Yes
Mutation: Yes
Other_details: Complexed With Cleaved Dna Duplex

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Ecorvr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Mm294
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbsrv
symmetry Space Group: P 1 21 1
R_factor 0.201 R_Free 0.262
length a length b length c angle alpha angle beta angle gamma
63.710 58.690 82.100 90.00 107.70 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand MN enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1BSS, 1RV5
A, B
  • nuclease activity
  • endonuclease activity

  • Primary referenceDNA Cleavage by EcoRV Endonuclease: Two Metal Ions in Three Metal Ion Binding Sites., Horton NC, Perona JJ, Biochemistry 2004 Jun 8;43(22):6841-57. PMID:15170321
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (1stx.pdb1.gz) 97 Kb
  • LPC: Ligand-Protein Contacts for 1STX
  • CSU: Contacts of Structural Units for 1STX
  • Likely Quarternary Molecular Structure file(s) for 1STX
  • Retrieve 1STX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1STX from S2C, [Save to disk]
  • View 1STX 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 1STX
  • 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 1STX, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1stxa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1stxb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1stx 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: [1stx_E] [1stx_F] [1stx_B] [1stx_D] [1stx_C] [1stx_A] [1stx]
  • SWISS-PROT database: [P04390]
  • Domain organization of [T2E5_ECOLX] by SWISSPFAM
  • Other resources with information on 1STX
  • Community annotation for 1STX 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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