5WZF Hydrolase date Jan 17, 2017
title Crystal Structure Of Mycobacterium Tuberculosis Vapc20 (Rv25 Sarcin-Ricin Loop Cleaving Toxin
authors K.G.Thakur, A.Deep
compound source
Molecule: 23s Rrna-Specific Endonuclease Vapc20
Chain: A
Synonym: Ribonuclease Vapc20,Rnase Vapc20,Toxin Vapc20
Ec: 3.1.-.-
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis (Strain Cdc Oshkosh);
Organism_taxid: 83331
Strain: Cdc 1551 Oshkosh
Gene: Vapc20, Mt2626.1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: 23s Rrna-Specific Endonuclease Vapc20
Chain: B
Synonym: Ribonuclease Vapc20,Rnase Vapc20,Toxin Vapc20
Ec: 3.1.-.-
Engineered: Yes

Organism_scientific: Mycobacterium Tuberculosis (Strain Cdc Oshkosh);
Organism_taxid: 83331
Strain: Cdc 1551 Oshkosh
Gene: Vapc20, Mt2626.1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: P 21 21 21
R_factor 0.171 R_Free 0.198
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.810 59.140 79.290 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand CSO enzyme Hydrolase E.C.3.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity
  • endoribonuclease activity
  • ribonuclease activity


  • Primary referenceCrystal structure of Mycobacterium tuberculosis VapC20 toxin and its interactions with cognate antitoxin, VapB20, suggest a model for toxin-antitoxin assembly., Deep A, Kaundal S, Agarwal S, Singh R, Thakur KG, FEBS J. 2017 Oct 7. doi: 10.1111/febs.14289. PMID:28986943
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (99 Kb) [Save to disk]
  • Biological Unit Coordinates (5wzf.pdb1.gz) 92 Kb
  • LPC: Ligand-Protein Contacts for 5WZF
  • CSU: Contacts of Structural Units for 5WZF
  • Structure Factors (650 Kb)
  • Retrieve 5WZF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5WZF from S2C, [Save to disk]
  • View 5WZF in 3D
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  • Visual 3D analysis of 5WZF
  • 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
  • Fold representative 5wzf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5wzf_B] [5wzf_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5WZF
  • Community annotation for 5WZF at PDBWiki (http://pdbwiki.org)

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