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- PDB-3gco: Crystal structure of DegS H198P/D320A mutant modified by DFP in c... -

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Basic information

Entry
Database: PDB / ID: 3gco
TitleCrystal structure of DegS H198P/D320A mutant modified by DFP in complex with DNRDGNVYQF OMP peptide
Components
  • DNRDGNVYQF peptide
  • Protease degS
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / protease / stress-sensor / HtrA / PDZ OMP / allostery / Hydrolase / Serine protease / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX
Function / homology
Function and homology information


peptidase Do / cellular response to misfolded protein / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.798 Å
AuthorsSohn, J. / Grant, R.A. / Sauer, R.T.
CitationJournal: Structure / Year: 2009
Title: OMP peptides activate the DegS stress-sensor protease by a relief of inhibition mechanism.
Authors: Sohn, J. / Grant, R.A. / Sauer, R.T.
History
DepositionFeb 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Mar 13, 2013Group: Other
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease degS
B: DNRDGNVYQF peptide


Theoretical massNumber of molelcules
Total (without water)37,4862
Polymers37,4862
Non-polymers00
Water00
1
A: Protease degS
B: DNRDGNVYQF peptide

A: Protease degS
B: DNRDGNVYQF peptide

A: Protease degS
B: DNRDGNVYQF peptide


Theoretical massNumber of molelcules
Total (without water)112,4586
Polymers112,4586
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9620 Å2
ΔGint-40 kcal/mol
Surface area41580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.408, 119.408, 119.408
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Protease degS


Mass: 36257.789 Da / Num. of mol.: 1 / Mutation: H198P,D320A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b3235, degS, hhoB, htrH, JW3204 / 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: Protein/peptide DNRDGNVYQF peptide


Mass: 1228.249 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3% PEG3350, 100 mM Bis-Tris propane, 40 mM NaF, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 2008
RadiationMonochromator: Varimax-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.798→59 Å / Num. obs: 14287 / % possible obs: 99.8 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.091 / Χ2: 0.991 / Net I/σ(I): 29.458
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.798-2.98.10.84614150.751100
2.9-3.0211.50.63514030.7651100
3.02-3.1512.20.45914140.8251100
3.15-3.3212.30.35214210.861100
3.32-3.5312.10.25814081.1861100
3.53-3.812.20.17314041.0911100
3.8-4.1812.10.1114501.2071100
4.18-4.7912.20.05814321.0951100
4.79-6.0312.20.05314500.9941100
6.03-5911.60.03114901.033198.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.798→24.374 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.839 / SU ML: 0.31 / σ(F): 0.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1366 9.99 %
Rwork0.211 --
obs0.214 13668 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.703 Å2 / ksol: 0.282 e/Å3
Displacement parametersBiso max: 266.99 Å2 / Biso mean: 116.911 Å2 / Biso min: 33.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.036 Å2-10.13 Å2-3.39 Å2
2---10.146 Å2-0.185 Å2
3----14.793 Å2
Refinement stepCycle: LAST / Resolution: 2.798→24.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 0 0 2294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032323
X-RAY DIFFRACTIONf_angle_d0.7153164
X-RAY DIFFRACTIONf_chiral_restr0.048381
X-RAY DIFFRACTIONf_plane_restr0.004421
X-RAY DIFFRACTIONf_dihedral_angle_d15.401851
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.798-2.8980.3021270.2731132125988
2.898-3.0140.2961330.2431150128391
3.014-3.1510.2421330.2331193132694
3.151-3.3160.3171290.2191219134895
3.316-3.5240.2491360.2251186132294
3.524-3.7950.241360.211226136298
3.795-4.1750.2161450.1941274141997
4.175-4.7750.2071410.1591279142099
4.775-6.0010.2341390.19612901429100
6.001-24.3750.2211470.22113531500100

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