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- PDB-2qf0: Structure of the delta PDZ truncation of the DegS protease -

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Basic information

Entry
Database: PDB / ID: 2qf0
TitleStructure of the delta PDZ truncation of the DegS protease
ComponentsProtease degS
KeywordsHYDROLASE / DegS / protease / periplasmic stress sensor / Htra / allosteric activation
Function / homology
Function and homology information


peptidase Do / cellular response to misfolded protein / serine-type peptidase activity / outer membrane-bounded periplasmic space / peptidase activity / 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 profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin / Trypsin-like serine proteases ...Peptidase S1C, DegS / PDZ domain / Peptidase S1C / Trypsin-like peptidase 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine endoprotease DegS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSohn, J. / Grant, R.A. / Sauer, R.T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Allosteric activation of DegS, a stress sensor PDZ protease.
Authors: Sohn, J. / Grant, R.A. / Sauer, R.T.
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease degS
B: Protease degS
C: Protease degS
D: Protease degS
E: Protease degS
F: Protease degS
G: Protease degS
H: Protease degS
I: Protease degS


Theoretical massNumber of molelcules
Total (without water)236,8989
Polymers236,8989
Non-polymers00
Water7,422412
1
A: Protease degS
B: Protease degS
C: Protease degS


Theoretical massNumber of molelcules
Total (without water)78,9663
Polymers78,9663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-19 kcal/mol
Surface area25510 Å2
MethodPISA, PQS
2
D: Protease degS
E: Protease degS
F: Protease degS


Theoretical massNumber of molelcules
Total (without water)78,9663
Polymers78,9663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-16 kcal/mol
Surface area24650 Å2
MethodPISA, PQS
3
G: Protease degS
H: Protease degS
I: Protease degS


Theoretical massNumber of molelcules
Total (without water)78,9663
Polymers78,9663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-19 kcal/mol
Surface area23490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.168, 132.974, 229.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protease degS


Mass: 26322.029 Da / Num. of mol.: 9 / Fragment: residues 27-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: degS, hhoB, htrH / Plasmid: pET21B / Production host: Escherichia coli (E. coli) / Strain (production host): X90(DE3)
References: UniProt: P0AEE3, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM NaCacodylate pH 6.5, 150 mM NaCitrate, 18% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2007 / Details: crystal monochromometer
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionRedundancy: 6 % / Av σ(I) over netI: 9.7 / Number: 868887 / Rmerge(I) obs: 0.099 / Χ2: 1.55 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 145473 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385099.610.0561.8897.1
4.275.3899.910.0722.1427.3
3.734.2799.910.0911.9027.4
3.393.7399.910.1221.7727
3.153.3910010.1511.3716.8
2.963.1510010.1791.1986.4
2.822.9610010.2371.0085.8
2.692.8299.910.330.9255.1
2.592.6999.210.4231.3713.9
2.52.5994.110.4391.1362.8
ReflectionResolution: 2.5→50 Å / Num. obs: 145473 / % possible obs: 99.2 % / Redundancy: 6 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.439 / % possible all: 94.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→42.53 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 81923.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 6824 4.9 %RANDOM
Rwork0.207 ---
obs0.207 138297 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.9829 Å2 / ksol: 0.302849 e/Å3
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13440 0 0 412 13852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 870 4.4 %
Rwork0.277 18734 -
obs--79.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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