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- PDB-2qf3: Structure of the delta PDZ truncation of the DegS protease -

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Basic information

Entry
Database: PDB / ID: 2qf3
TitleStructure of the delta PDZ truncation of the DegS protease
ComponentsProtease degS
KeywordsHYDROLASE / DegS / protease / periplasmic stress sensor / Htra / allosteric activation
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
PHOSPHATE ION / Serine endoprotease DegS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsSohn, J. / Grant, R.A. / Sauer, R.T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Allosteric activation of DegS, a stress sensor PDZ protease.
Authors: Sohn, J. / Grant, R.A. / Sauer, R.T.
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)78,6886
Polymers78,4033
Non-polymers2853
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-40 kcal/mol
Surface area24030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.347, 75.316, 162.257
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: 26134.449 Da / Num. of mol.: 3 / Fragment: residues 27-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: degS, hhoB, htrH / 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 / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 0.2 M ammonium phosphate (monobasic), 0.1 M Tris pH 8.5, 30% methylpentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 11, 2007 / Details: Rigaku Varimax-HR
RadiationMonochromator: Varimax-HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 6.7 % / Av σ(I) over netI: 11 / Number: 377604 / Rmerge(I) obs: 0.067 / Χ2: 1.5 / D res high: 2.04 Å / D res low: 50 Å / Num. obs: 56302 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.395099.210.0422.2686.8
3.494.3910010.0613.057.1
3.053.4910010.0752.3757.2
2.773.0510010.0951.6997.3
2.572.7710010.1281.2097.4
2.422.5710010.170.9347.4
2.32.4210010.2340.7387.3
2.22.399.910.2980.6576.8
2.112.297.810.3690.5875.4
2.042.1183.810.4680.5363.7
ReflectionResolution: 2.04→50 Å / Num. obs: 56302 / % possible obs: 98.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 11
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.468 / % possible all: 83.8

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Phasing

Phasing MRRfactor: 0.373 / Cor.coef. Fo:Fc: 0.714 / Cor.coef. Io to Ic: 0.707
Highest resolutionLowest resolution
Rotation3.011 Å15 Å
Translation3.011 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2QF0, chains A,B,C

2qf0


Resolution: 2.04→32.61 Å / Rfactor Rfree error: 0.004
RfactorNum. reflection% reflection
Rfree0.219 2598 4.9 %
Rwork0.189 --
obs0.189 53038 92.8 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.75 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 44.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å20 Å2
2---2.76 Å20 Å2
3---0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.04→32.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 15 305 4776
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.621.5
X-RAY DIFFRACTIONc_mcangle_it2.642
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.04→2.17 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.283 393 5.4 %
Rwork0.242 6946 -
obs--78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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