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- PDB-3lgi: Structure of the protease domain of DegS (DegS-deltaPDZ) at 1.65 A -

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Basic information

Entry
Database: PDB / ID: 3lgi
TitleStructure of the protease domain of DegS (DegS-deltaPDZ) at 1.65 A
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
PHOSPHATE ION / Serine endoprotease DegS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 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 20, 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 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease degS
B: Protease degS
C: Protease degS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7855
Polymers76,5953
Non-polymers1902
Water15,061836
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-37 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.384, 72.762, 128.877
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: 25531.799 Da / Num. of mol.: 3 / Fragment: protease domain
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 836 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 40-100 mM Sodium Cacodylate, 10-20 % isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2009 / Details: crystal monochrometer
RadiationMonochromator: 24id-c / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.65→100 Å / Num. obs: 79543 / % possible obs: 99.6 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.65-1.684.20.48194.8
1.68-1.714.70.42997.8
1.71-1.745.40.3899.3
1.74-1.7811.10.317100
1.78-1.8214.70.257100
1.82-1.8614.70.219100
1.86-1.914.70.177100
1.9-1.9614.70.142100
1.96-2.0114.70.123100
2.01-2.0814.70.107100
2.08-2.1514.70.092100
2.15-2.2414.80.084100
2.24-2.3414.70.078100
2.34-2.4614.70.072100
2.46-2.6214.70.064100
2.62-2.8214.60.062100
2.82-3.1114.50.06100
3.11-3.55140.061100
3.55-4.4813.80.048100
4.48-10013.40.04199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.652→31.681 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.17 / σ(F): 1.34 / Phase error: 15.84 / 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
Rfree0.1815 3982 5.01 %
Rwork0.1519 --
obs0.1534 79450 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.204 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 22.275 Å2
Baniso -1Baniso -2Baniso -3
1--1.644 Å20 Å20 Å2
2--0.737 Å2-0 Å2
3---0.763 Å2
Refinement stepCycle: LAST / Resolution: 1.652→31.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4899 0 10 836 5745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055213
X-RAY DIFFRACTIONf_angle_d1.0397147
X-RAY DIFFRACTIONf_dihedral_angle_d15.4561938
X-RAY DIFFRACTIONf_chiral_restr0.067868
X-RAY DIFFRACTIONf_plane_restr0.005950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.652-1.67240.22471160.19552397X-RAY DIFFRACTION89
1.6724-1.69360.2238990.19112593X-RAY DIFFRACTION96
1.6936-1.71590.21621320.1822655X-RAY DIFFRACTION98
1.7159-1.73940.2091620.16862645X-RAY DIFFRACTION99
1.7394-1.76420.17871200.16732687X-RAY DIFFRACTION100
1.7642-1.79060.19221520.14982670X-RAY DIFFRACTION100
1.7906-1.81850.19431670.14512671X-RAY DIFFRACTION100
1.8185-1.84830.15041370.14542664X-RAY DIFFRACTION100
1.8483-1.88020.19161210.14212718X-RAY DIFFRACTION100
1.8802-1.91440.18421500.14712672X-RAY DIFFRACTION100
1.9144-1.95120.18391640.14532681X-RAY DIFFRACTION100
1.9512-1.9910.19421440.1462667X-RAY DIFFRACTION100
1.991-2.03430.17651540.14582677X-RAY DIFFRACTION100
2.0343-2.08160.21121380.13892711X-RAY DIFFRACTION100
2.0816-2.13370.16151600.13482668X-RAY DIFFRACTION100
2.1337-2.19140.16361640.13512681X-RAY DIFFRACTION100
2.1914-2.25580.18091370.13682703X-RAY DIFFRACTION100
2.2558-2.32860.15441220.13812737X-RAY DIFFRACTION100
2.3286-2.41180.16461410.13322708X-RAY DIFFRACTION100
2.4118-2.50830.1671350.13722720X-RAY DIFFRACTION100
2.5083-2.62240.16951420.1372705X-RAY DIFFRACTION100
2.6224-2.76060.1841390.14492727X-RAY DIFFRACTION100
2.7606-2.93350.16191340.1462757X-RAY DIFFRACTION100
2.9335-3.15980.17181480.14032733X-RAY DIFFRACTION100
3.1598-3.47740.17451270.14462764X-RAY DIFFRACTION100
3.4774-3.97980.17611470.13552759X-RAY DIFFRACTION100
3.9798-5.01090.1471540.12792789X-RAY DIFFRACTION100
5.0109-31.68680.20761760.21172909X-RAY DIFFRACTION100

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