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- PDB-1sot: Crystal Structure of the DegS stress sensor -

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Basic information

Entry
Database: PDB / ID: 1sot
TitleCrystal Structure of the DegS stress sensor
ComponentsProtease degS
KeywordsHYDROLASE / stress response / protein quality control / PDZ / UPR / HtrA
Function / homology
Function and homology information


: / peptidase Do / cellular response to misfolded protein / membrane => GO:0016020 / serine-type peptidase activity / peptidase activity / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Peptidase S1C, DegS / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...Peptidase S1C, DegS / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine endoprotease DegS / Serine endoprotease DegS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWilken, C. / Kitzing, K. / Kurzbauer, R. / Ehrmann, M. / Clausen, T.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2004
Title: Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease
Authors: Wilken, C. / Kitzing, K. / Kurzbauer, R. / Ehrmann, M. / Clausen, T.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: OMP peptide signals initiate the envelope stress response by activating DegS protease via relief of inhibition mediated by its PDZ domain
Authors: Walsh, N.P. / Alba, B.M. / Bose, B. / Gross, C.A. / Sauer, R.T.
History
DepositionMar 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease degS
B: Protease degS
C: Protease degS


Theoretical massNumber of molelcules
Total (without water)103,0623
Polymers103,0623
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-27 kcal/mol
Surface area37000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.681, 143.062, 41.529
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protease degS


Mass: 34353.898 Da / Num. of mol.: 3 / Fragment: protease plus PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DEGS, HHOB, HTRH, B3235, Z4594, ECS4108 / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P31137, UniProt: P0AEE3*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 6000, MPD, magnesium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292.K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. all: 51588 / Num. obs: 51588 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.049 / Net I/σ(I): 24.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.93 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.205 / % possible all: 99.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KY9

1ky9


Resolution: 2.3→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 2510 random
Rwork0.198 --
all0.201 51588 -
obs0.201 51588 -
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6287 0 0 330 6617
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_bond_d0.012

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