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- PDB-3b8j: Q191A mutant of DegS-deltaPDZ -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3b8j
TitleQ191A mutant of DegS-deltaPDZ
ComponentsProtease degS
KeywordsHYDROLASE / DegS / protease / periplasmic stress sensor / HTRA / allosteric activation / Serine protease
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-like serine proteases / Thrombin, subunit H ...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-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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.507 Å
AuthorsGrant, R.A. / Sohn, J. / Sauer, R.T.
CitationJournal: To be Published
Title: biochemical characterization of DegS-deltaPDZ q191A mutant
Authors: Sohn, J. / Grant, R.A. / Sauer, R.T.
History
DepositionNov 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease degS


Theoretical massNumber of molelcules
Total (without water)26,0771
Polymers26,0771
Non-polymers00
Water0
1
A: Protease degS

A: Protease degS

A: Protease degS


Theoretical massNumber of molelcules
Total (without water)78,2323
Polymers78,2323
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area4370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.892, 70.892, 120.837
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Protease degS


Mass: 26077.398 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-256 / Mutation: Q191A
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

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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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM Na Cacodylate, 150 mM NaCitrate, 18% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 6682 / % possible obs: 85.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.058 / Χ2: 1.695 / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.163 / Num. unique all: 419 / Χ2: 0.573 / % possible all: 54

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PHENIXrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.507→27.367 Å / FOM work R set: 0.645 / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.273 643 9.69 %
Rwork0.234 --
obs-6637 42.72 %
Solvent computationBsol: 54.682 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso max: 140.91 Å2 / Biso mean: 78.44 Å2 / Biso min: 49.49 Å2
Baniso -1Baniso -2Baniso -3
1--32.357 Å20 Å20 Å2
2---32.357 Å20 Å2
3---64.714 Å2
Refinement stepCycle: LAST / Resolution: 2.507→27.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 0 0 1351
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.721
X-RAY DIFFRACTIONf_bond_d0.0031
X-RAY DIFFRACTIONf_chiral_restr0.0461
X-RAY DIFFRACTIONf_dihedral_angle_d15.7161
X-RAY DIFFRACTIONf_plane_restr0.0031
X-RAY DIFFRACTIONf_nbd_refined4.1171
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.507-2.580.314309X-RAY DIFFRACTION1225
2.58-2.6640.287344X-RAY DIFFRACTION1227
2.664-2.7590.31415X-RAY DIFFRACTION1232
2.759-2.8690.286439X-RAY DIFFRACTION1234
2.869-2.9990.276488X-RAY DIFFRACTION1237
2.999-3.1570.265526X-RAY DIFFRACTION1241
3.157-3.3550.25600X-RAY DIFFRACTION1245
3.355-3.6130.248570X-RAY DIFFRACTION1244
3.613-3.9760.235552X-RAY DIFFRACTION1243
3.976-4.5490.187584X-RAY DIFFRACTION1245
4.549-5.7220.206587X-RAY DIFFRACTION1245
5.722-27.3690.213580X-RAY DIFFRACTION1244

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