2VLA Hydrolase date Jan 11, 2008
title Crystal Structure Of Restriction Endonuclease Bpuji Recognition Domain In Complex With Cognate Dna
authors R.Sukackaite, S.Grazulis, M.Bochtler, V.Siksnys
compound source
Molecule: Restriction Endonuclease R.Bpuji
Chain: A
Fragment: Recognition Domain, Residues 1-285
Synonym: Bpuji
Ec: 3.1.21.4
Engineered: Yes
Organism_scientific: Bacillus Pumilus
Organism_taxid: 1408
Strain: Rfl1458
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Er2267
Expression_system_plasmid: Pal-Bpuji

Molecule: 5'-D(Gpgptpapcpcpcpgptpgp Gpa)-3'
Chain: L
Engineered: Yes

Synthetic: Yes
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'-D(Tpcpcpapcpgpgpgptpap Cpc)-3'
Chain: M

Synthetic: Yes
symmetry Space Group: P 21 21 2
R_factor 0.138 R_Free 0.166
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.292 167.513 43.846 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.30 Å
ligand NA, PG6 enzyme Hydrolase E.C.3.1.21.4 BRENDA
note 2VLA is a representative structure
Primary referenceThe recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution., Sukackaite R, Grazulis S, Bochtler M, Siksnys V, J Mol Biol. 2008 May 16;378(5):1084-93. Epub 2008 Mar 28. PMID:18433771
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (2vla.pdb1.gz) 138 Kb
  • LPC: Ligand-Protein Contacts for 2VLA
  • CSU: Contacts of Structural Units for 2VLA
  • Likely Quarternary Molecular Structure file(s) for 2VLA
  • Structure Factors (684 Kb)
  • Retrieve 2VLA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VLA from S2C, [Save to disk]
  • Re-refined 2vla structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VLA 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 2VLA
  • 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 2VLA, from MSDmotif at EBI
  • Fold representative 2vla from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vla_M] [2vla_A] [2vla] [2vla_L]
  • SWISS-PROT database: [A3FMN7]
  • Domain organization of [A3FMN7_BACPU] by SWISSPFAM
  • Other resources with information on 2VLA
  • Community annotation for 2VLA 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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