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

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Basic information

Entry
Database: PDB / ID: 3gds
TitleCrystal structure of DegS H198P/D320A mutant modified by DFP in complex with DNRDGNVYYF peptide
Components
  • DNRDGNVYYF peptide
  • Protease degS
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / protease / stress-sensor / HtrA / PDZ OMP / 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 / Resolution: 2.85 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 24, 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 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Protease degS
B: DNRDGNVYYF peptide


Theoretical massNumber of molelcules
Total (without water)37,5212
Polymers37,5212
Non-polymers00
Water00
1
A: Protease degS
B: DNRDGNVYYF peptide

A: Protease degS
B: DNRDGNVYYF peptide

A: Protease degS
B: DNRDGNVYYF peptide


Theoretical massNumber of molelcules
Total (without water)112,5636
Polymers112,5636
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9750 Å2
ΔGint-38 kcal/mol
Surface area38900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.822, 118.822, 118.822
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 / Fragment: full-length without membrane anchor / 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 DNRDGNVYYF peptide


Mass: 1263.294 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: 3.73 Å3/Da / Density % sol: 66.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM Bis-Tris propane, 100 mM NaF, 5 % PEG 3350, 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
RadiationMonochromator: Varimax-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→100 Å / Num. obs: 13350 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.075 / Χ2: 1.05 / Net I/σ(I): 31.18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.85-2.957.90.5413130.688199.9
2.95-3.079.40.39412990.7151100
3.07-3.219.40.30713230.7841100
3.21-3.389.40.21813300.831100
3.38-3.599.40.15513350.9571100
3.59-3.879.40.10813171.0371100
3.87-4.269.40.07113241.2521100
4.26-4.879.40.05113341.4851100
4.87-6.149.30.04613601.2811100
6.14-1008.80.03114151.395198.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementResolution: 2.85→32.955 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.848 / SU ML: 0.32 / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1269 9.95 %
Rwork0.209 --
obs0.21 12754 95.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.762 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 297.49 Å2 / Biso mean: 92.576 Å2 / Biso min: 15.48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.85→32.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 0 0 2236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042265
X-RAY DIFFRACTIONf_angle_d0.8053087
X-RAY DIFFRACTIONf_chiral_restr0.056373
X-RAY DIFFRACTIONf_plane_restr0.004409
X-RAY DIFFRACTIONf_dihedral_angle_d14.546821
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.9630.3771210.2641182130389
2.963-3.0980.2791270.2341174130191
3.098-3.2610.2681450.2321235138094
3.261-3.4660.2761390.2131264140395
3.466-3.7330.2041460.2041292143897
3.733-4.1080.2221490.1921286143597
4.108-4.7010.1631470.1571312145999
4.701-5.9170.1921460.1881342148899
5.917-32.9580.1921490.2221398154799

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