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- PDB-6ew9: CRYSTAL STRUCTURE OF DEGS STRESS SENSOR PROTEASE IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 6ew9
TitleCRYSTAL STRUCTURE OF DEGS STRESS SENSOR PROTEASE IN COMPLEX WITH ACTIVATING DNRLGLVYQF PEPTIDE
Components
  • DNRLGLVYQF PEPTIDE
  • Serine endoprotease DegS
KeywordsHYDROLASE / PROTEASE / STRESS-SENSOR / PDZ / PERIPLASM / SERINE PROTEIASE / ACTIVATOR PEPTIDE
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 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Trypsin ...Peptidase S1C, DegS / PDZ domain / Peptidase S1C / Trypsin-like peptidase 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Serine endoprotease DegS
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVetter, I.R. / Porfetye, A.T. / Stege, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCRC1093 Germany
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Identification of Noncatalytic Lysine Residues from Allosteric Circuits via Covalent Probes.
Authors: Bongard, J. / Lorenz, M. / Vetter, I.R. / Stege, P. / Porfetye, A.T. / Schmitz, A.L. / Kaschani, F. / Wolf, A. / Koch, U. / Nussbaumer, P. / Klebl, B. / Kaiser, M. / Ehrmann, M.
History
DepositionNov 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 7, 2018Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine endoprotease DegS
B: Serine endoprotease DegS
C: Serine endoprotease DegS
P: DNRLGLVYQF PEPTIDE
Q: DNRLGLVYQF PEPTIDE
R: DNRLGLVYQF PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,90315
Polymers103,4766
Non-polymers4279
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-127 kcal/mol
Surface area38490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.600, 53.650, 132.500
Angle α, β, γ (deg.)90.000, 101.800, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Serine endoprotease DegS / Site-1 protease DegS / S1P protease DegS / Site-1-type intramembrane protease


Mass: 33266.633 Da / Num. of mol.: 3 / Fragment: PROTEASE AND PDZ DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: degS, hhoB, htrH, b3235, JW3204 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon +RIL / References: UniProt: P0AEE3, peptidase Do
#2: Protein/peptide DNRLGLVYQF PEPTIDE


Mass: 1225.374 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.5 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 14.4% PEG 8000, 160 mM CaAc, 80 mM Na-cacodylate pH 6.5, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→129.699 Å / Num. obs: 50358 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.72 % / Biso Wilson estimate: 45.998 Å2 / Rmerge(I) obs: 0.162 / Rrim(I) all: 0.175 / Net I/σ(I): 8.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
2.2-2.266.591.4930.9436801.6299.6
2.26-2.321.3011.1136251.41799.8
2.32-2.391.1631.3135061.25699.9
2.39-2.461.0021.634051.08199.9
2.46-2.540.8241.9533230.8999.8
2.54-2.630.672.432030.72499.8
2.63-2.730.5552.8330610.60299.8
2.73-2.840.4563.4629770.49899.9
2.84-2.970.344.9328650.36799.8
2.97-3.110.2626.627320.28399.5
3.11-3.280.2098.225740.22699.9
3.28-3.480.1510.7924840.16299.8
3.48-3.720.11813.0523130.12999.7
3.72-4.020.09716.9921630.10599.5
4.02-4.40.07222.6619900.07899.4
4.4-4.920.06324.8518300.06999.7
4.92-5.680.07321.2115850.0899.5
5.68-6.960.07123.0713610.07799.1
6.96-9.840.04830.2810690.05299.1
9.840.03338.666120.03797.9

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.382 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.52
RfactorNum. reflection% reflection
Rfree0.2731 2518 5.01 %
Rwork0.2256 --
obs0.228 50307 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.25 Å2 / Biso mean: 52.6065 Å2 / Biso min: 23.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6819 0 15 80 6914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.24250.39931390.351126442783100
2.2425-2.28820.36571360.335526152751100
2.2882-2.3380.36051380.313226352773100
2.338-2.39240.39431380.309926332771100
2.3924-2.45220.33981410.296426442785100
2.4522-2.51850.34981380.284126052743100
2.5185-2.59260.31721390.266126522791100
2.5926-2.67630.3761390.270526712810100
2.6763-2.77190.31551370.255226132750100
2.7719-2.88280.29091420.247426692811100
2.8828-3.0140.27621400.24226372777100
3.014-3.17290.28311420.238226542796100
3.1729-3.37160.30941380.234926502788100
3.3716-3.63180.26831400.219526762816100
3.6318-3.99710.26471400.206426562796100
3.9971-4.57490.21381410.173326732814100
4.5749-5.76180.21361410.188126922833100
5.7618-43.39020.23311490.19692770291999

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