1SOZ Hydrolase date Mar 16, 2004
title Crystal Structure Of Degs Protease In Complex With An Activating Peptide
authors C.Wilken, K.Kitzing, R.Kurzbauer, M.Ehrmann, T.Clausen
compound source
Molecule: Protease Degs
Chain: A, B, C
Ec: 3.4.21.-
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Degs, Hhob, Htrh, B3235, Z4594, Ecs4108
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21b

Molecule: Activating Peptide
Chain: D, E
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.213 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
205.984 142.710 41.167 90.00 89.24 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand
enzyme Hydrolase E.C.3.4.21 BRENDA
related structures by homologous chain: 1SOT
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceCrystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease., Wilken C, Kitzing K, Kurzbauer R, Ehrmann M, Clausen T, Cell 2004 May 14;117(4):483-94. PMID:15137941
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (1soz.pdb1.gz) 128 Kb
  • CSU: Contacts of Structural Units for 1SOZ
  • Likely Quarternary Molecular Structure file(s) for 1SOZ
  • Structure Factors (352 Kb)
  • Retrieve 1SOZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SOZ from S2C, [Save to disk]
  • Re-refined 1soz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SOZ 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 1SOZ
  • 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 1SOZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1soza1, region A:255-352 [Jmol] [rasmolscript] [script source]
        - Domain d1soza2, region A:42-254 [Jmol] [rasmolscript] [script source]
        - Domain d1sozb1, region B:255-353 [Jmol] [rasmolscript] [script source]
        - Domain d1sozb2, region B:42-254 [Jmol] [rasmolscript] [script source]
        - Domain d1sozc1, region C:255-353 [Jmol] [rasmolscript] [script source]
        - Domain d1sozc2, region C:42-254 [Jmol] [rasmolscript] [script source]
  • Fold representative 1soz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1soz] [1soz_E] [1soz_D] [1soz_A] [1soz_B] [1soz_C]
  • SWISS-PROT database: [P0AEE3]
  • Domain organization of [DEGS_ECOLI] by SWISSPFAM
  • Domain found in 1SOZ: [PDZ ] by SMART
  • Other resources with information on 1SOZ
  • Community annotation for 1SOZ 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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