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- PDB-3lgv: H198P mutant of the DegS-deltaPDZ protease -

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Basic information

Entry
Database: PDB / ID: 3lgv
TitleH198P mutant of the DegS-deltaPDZ protease
ComponentsProtease degS
KeywordsHYDROLASE / protease / stress-sensor / HtrA / PDZ OMP / 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 / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.734 Å
AuthorsSohn, J. / Grant, R.A. / Sauer, R.T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Allostery is an intrinsic property of the protease domain of DegS: implications for enzyme function and evolution.
Authors: Sohn, J. / Grant, R.A. / Sauer, R.T.
History
DepositionJan 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 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
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)232,6429
Polymers232,6429
Non-polymers00
Water3,747208
1
A: Protease degS
B: Protease degS
C: Protease degS


Theoretical massNumber of molelcules
Total (without water)77,5473
Polymers77,5473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-16 kcal/mol
Surface area25690 Å2
MethodPISA
2
D: Protease degS
E: Protease degS
F: Protease degS


Theoretical massNumber of molelcules
Total (without water)77,5473
Polymers77,5473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-15 kcal/mol
Surface area24570 Å2
MethodPISA
3
G: Protease degS
H: Protease degS
I: Protease degS


Theoretical massNumber of molelcules
Total (without water)77,5473
Polymers77,5473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-17 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.540, 133.565, 230.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protease degS


Mass: 25849.145 Da / Num. of mol.: 9 / Fragment: protease domain / Mutation: h198p
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM Sodium Cacodylate, 50-125 Sodium Citrate, 10-20 % isopropanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5416 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 10, 2009 / Details: Varimax-HF
RadiationMonochromator: Varimax-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5416 Å / Relative weight: 1
ReflectionResolution: 2.734→50 Å / Num. obs: 55922 / % possible obs: 94.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.734-2.855.30.50295.9
2.85-2.965.30.37295.4
2.96-3.15.30.26894.6
3.1-3.265.40.21394.2
3.26-3.465.50.16693.2
3.46-3.735.50.13292.1
3.73-4.115.50.11191
4.11-4.75.40.08293.6
4.7-5.9260.07199.6
5.92-506.30.04899.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.734→33.819 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.4 / σ(F): 1.34 / Phase error: 28.69 / Stereochemistry target values: ML
Details: To obtain the best possible geometry, this structure was refined with hydrogens whose coordinates were determined by the attached heavy atom. Authors state that although hydrogens cannot be ...Details: To obtain the best possible geometry, this structure was refined with hydrogens whose coordinates were determined by the attached heavy atom. Authors state that although hydrogens cannot be visualized at this resolution, they are present and contribute to scattering. The hydrogens are kept in this entry because independent assessment of many aspects of the geometry, including steric clashes, require their presence. Moreover, removing hydrogen atoms after refinement makes independent assessment of refinement statistics effectively irreproducible.
RfactorNum. reflection% reflection
Rfree0.2699 2852 5.11 %
Rwork0.2194 --
obs0.222 55770 94.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.855 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso mean: 56.528 Å2
Baniso -1Baniso -2Baniso -3
1-1.626 Å2-0 Å20 Å2
2---1.757 Å2-0 Å2
3---0.131 Å2
Refinement stepCycle: LAST / Resolution: 2.734→33.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13375 0 0 208 13583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413536
X-RAY DIFFRACTIONf_angle_d0.79318407
X-RAY DIFFRACTIONf_dihedral_angle_d14.0924871
X-RAY DIFFRACTIONf_chiral_restr0.0442246
X-RAY DIFFRACTIONf_plane_restr0.0042428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.734-2.78140.34681100.26322227X-RAY DIFFRACTION80
2.7814-2.83190.30741360.25822659X-RAY DIFFRACTION96
2.8319-2.88640.3261420.24852639X-RAY DIFFRACTION95
2.8864-2.94520.3441460.24052644X-RAY DIFFRACTION96
2.9452-3.00920.28491620.23442621X-RAY DIFFRACTION95
3.0092-3.07920.32351340.2182634X-RAY DIFFRACTION95
3.0792-3.15620.28121400.21932641X-RAY DIFFRACTION94
3.1562-3.24140.32511490.22672616X-RAY DIFFRACTION94
3.2414-3.33670.31421440.22472579X-RAY DIFFRACTION93
3.3367-3.44430.26831380.21672606X-RAY DIFFRACTION93
3.4443-3.56730.25791560.21232573X-RAY DIFFRACTION93
3.5673-3.710.27291400.2122548X-RAY DIFFRACTION91
3.71-3.87860.28351140.21762567X-RAY DIFFRACTION91
3.8786-4.08270.24191300.20482545X-RAY DIFFRACTION90
4.0827-4.3380.22451390.17662588X-RAY DIFFRACTION92
4.338-4.67220.20871540.15882671X-RAY DIFFRACTION95
4.6722-5.14090.19621390.17352847X-RAY DIFFRACTION99
5.1409-5.88140.25951550.19592841X-RAY DIFFRACTION100
5.8814-7.39720.26721670.23252875X-RAY DIFFRACTION100
7.3972-33.8220.26871570.24592997X-RAY DIFFRACTION99

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