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- PDB-3lgu: Y162A mutant of the DegS-deltaPDZ protease -

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Basic information

Entry
Database: PDB / ID: 3lgu
TitleY162A 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 / 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 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: 2.46 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 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 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 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease degS


Theoretical massNumber of molelcules
Total (without water)25,7981
Polymers25,7981
Non-polymers00
Water50428
1
A: Protease degS

A: Protease degS

A: Protease degS


Theoretical massNumber of molelcules
Total (without water)77,3943
Polymers77,3943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)70.555, 70.555, 118.326
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: 25798.080 Da / Num. of mol.: 1 / Fragment: protease domain / Mutation: y162a
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


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM Sodium Cacodylate, 50-125 mM Sodium Citrate, 10-20% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING 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-HR
RadiationMonochromator: Varimax-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5416 Å / Relative weight: 1
ReflectionResolution: 2.46→50 Å / Num. obs: 7821 / % possible obs: 97.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.043 / Χ2: 1.131 / Net I/σ(I): 19.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.46-2.555.30.1317810.29799.2
2.55-2.655.50.1037970.34699.5
2.65-2.775.50.0948070.45699.8
2.77-2.925.50.0738030.61999.9
2.92-3.15.60.0647920.92299.9
3.1-3.345.60.0558181.24299.9
3.34-3.6750.0516131.51778.9
3.67-4.215.50.0488022.2199.5
4.21-5.35.70.0378081.936100
5.3-505.70.0358001.77799

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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: 2.46→22.667 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.779 / SU ML: 0.32 / σ(F): 1.97 / 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
Rfree0.246 354 4.54 %
Rwork0.21 --
obs0.211 7790 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.975 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 173.1 Å2 / Biso mean: 81.239 Å2 / Biso min: 34.84 Å2
Baniso -1Baniso -2Baniso -3
1--17.631 Å2-0 Å20 Å2
2---17.631 Å2-0 Å2
3---35.262 Å2
Refinement stepCycle: LAST / Resolution: 2.46→22.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 0 28 1417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031409
X-RAY DIFFRACTIONf_angle_d0.7671912
X-RAY DIFFRACTIONf_chiral_restr0.043237
X-RAY DIFFRACTIONf_plane_restr0.003249
X-RAY DIFFRACTIONf_dihedral_angle_d14.253504
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.46-2.550.3121350.2512513264899
2.81-3.5380.3161110.2082537264899
3.538-22.6680.2051080.1972386249494

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