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- PDB-3gdv: Crystal structure of DegS H198P/D320A mutant modified by DFP and ... -

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Basic information

Entry
Database: PDB / ID: 3gdv
TitleCrystal structure of DegS H198P/D320A mutant modified by DFP and in complex with YQF peptide
Components
  • DegS protease
  • YQF peptide
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / protease / stress-sensor / HtrA / PDZ OMP / Hydrolase / Serine protease / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX
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 / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...Peptidase S1C, DegS / PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / Pdz3 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 / Roll / 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 / SYNCHROTRON / Resolution: 2.489 Å
AuthorsSohn, J. / Grant, R.A. / Sauer, R.T.
CitationJournal: Structure / Year: 2009
Title: OMP peptides activate the DegS stress-sensor protease by a relief of inhibition mechanism.
Authors: Sohn, J. / Grant, R.A. / Sauer, R.T.
History
DepositionFeb 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Mar 13, 2013Group: Other
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DegS protease
B: DegS protease
C: DegS protease
D: YQF peptide
E: YQF peptide
F: YQF peptide


Theoretical massNumber of molelcules
Total (without water)110,1436
Polymers110,1436
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-37 kcal/mol
Surface area38310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.880, 172.278, 114.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DegS protease


Mass: 36257.789 Da / Num. of mol.: 3 / Fragment: full-length without membrane anchor / Mutation: H198P,D320A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia Coli (E. coli) / Strain: K-12 / 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: Protein/peptide YQF peptide


Mass: 456.492 Da / Num. of mol.: 3 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM Tris 100mM MgCl2 3% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2008 / Details: crystal monochrometer
RadiationMonochromator: crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.489→50 Å / Num. obs: 39897 / % possible obs: 96.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.967
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.489-2.593.90.24379.1
2.59-2.6940.22491.9
2.69-2.824.30.18498.5
2.82-2.964.50.15199.5
2.96-3.154.50.12199.6
3.15-3.394.50.10699.6
3.39-3.734.50.09699.4
3.73-4.274.50.08899.1
4.27-5.384.30.0799.2
5.38-504.30.04997.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementResolution: 2.489→32.039 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / σ(F): 1.37 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 2002 5.02 %
Rwork0.1912 --
obs0.1928 39869 95.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.755 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso mean: 73.72 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.489→32.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6584 0 0 78 6662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056663
X-RAY DIFFRACTIONf_angle_d0.839067
X-RAY DIFFRACTIONf_dihedral_angle_d14.6362429
X-RAY DIFFRACTIONf_chiral_restr0.0561100
X-RAY DIFFRACTIONf_plane_restr0.0031195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.489-2.55140.26021130.21071945X-RAY DIFFRACTION70
2.5514-2.62030.25251130.21232430X-RAY DIFFRACTION87
2.6203-2.69740.23491270.20922652X-RAY DIFFRACTION95
2.6974-2.78440.26111460.21442739X-RAY DIFFRACTION99
2.7844-2.88380.2531570.222766X-RAY DIFFRACTION99
2.8838-2.99920.26911720.21622782X-RAY DIFFRACTION99
2.9992-3.13560.25771580.20562754X-RAY DIFFRACTION100
3.1356-3.30080.28311430.20612823X-RAY DIFFRACTION100
3.3008-3.50730.23031320.18852811X-RAY DIFFRACTION99
3.5073-3.77780.22221530.18332778X-RAY DIFFRACTION99
3.7778-4.15720.19641370.17892818X-RAY DIFFRACTION99
4.1572-4.75710.16381390.14632840X-RAY DIFFRACTION99
4.7571-5.9870.20881530.17212834X-RAY DIFFRACTION99
5.987-32.04130.20021590.19212895X-RAY DIFFRACTION97
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.48150.2366-0.39490.9795-0.39930.72930.0797-0.1817-0.2528-0.0382-0.3318-0.17880.11370.25650.23040.03360.03380.00680.15330.14590.4065-15.000974.15176.7074
20.12980.11080.0299-0.284-0.1320.1043-0.0649-0.0075-0.3798-0.11480.0310.0181-0.0197-0.060.02740.88050.15620.06580.57480.27911.2818
30.84440.6366-0.08360.36790.09671.05220.28340.1061-0.7898-0.19680.0502-0.56970.04520.7563-0.30160.36790.21710.13760.7707-0.0731.2079
40.464-0.18920.26150.14430.3550.6282-0.17090.1166-0.2752-0.1030.03330.1282-0.0668-0.18090.14840.3044-0.13780.05170.3567-0.20940.5054
50.18540.2123-0.0745-0.2117-0.3890.0405-0.0774-0.0214-0.0027-0.0019-0.0649-0.0591-0.05070.04290.131.52540.159-0.06881.46930.27731.6305
60.4337-0.18410.1547-0.2003-0.0577-0.06470.0289-0.04060.0465-0.02870.0279-0.02990.00650.0391-0.04581.33870.15140.26591.4555-0.03862.2577
70.04530.071-0.12790.1181-0.1389-0.09340.024-0.02340.00870.0184-0.06980.12320.0481-0.01710.04050.7475-0.23850.16840.6683-0.18360.776
Refinement TLS groupSelection details: Chain F

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