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- PDB-6jjk: Crystal structure of the DegP dodecamer with a modulator -

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Basic information

Entry
Database: PDB / ID: 6jjk
TitleCrystal structure of the DegP dodecamer with a modulator
Components
  • CYS-TYR-TYR-LYS-ILE
  • Periplasmic serine endoprotease DegP
KeywordsHYDROLASE
Function / homology
Function and homology information


peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / : / serine-type peptidase activity / protein folding / peptidase activity / outer membrane-bounded periplasmic space / response to heat / response to oxidative stress ...peptidase Do / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / : / serine-type peptidase activity / protein folding / peptidase activity / outer membrane-bounded periplasmic space / response to heat / response to oxidative stress / periplasmic space / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Peptidase S1C, Do / 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 / Peptidase S1, PA clan
Similarity search - Domain/homology
Periplasmic serine endoprotease DegP
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsCho, H. / Choi, Y. / Lee, H.H. / Kim, S.
CitationJournal: Commun Biol / Year: 2020
Title: Over-activation of a nonessential bacterial protease DegP as an antibiotic strategy
Authors: Cho, H. / Choi, Y. / Min, K. / Son, J.B. / Park, H. / Lee, H.H. / Kim, S.
History
DepositionFeb 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic serine endoprotease DegP
B: Periplasmic serine endoprotease DegP
C: Periplasmic serine endoprotease DegP
D: Periplasmic serine endoprotease DegP
E: Periplasmic serine endoprotease DegP
F: Periplasmic serine endoprotease DegP
G: CYS-TYR-TYR-LYS-ILE
H: CYS-TYR-TYR-LYS-ILE
I: CYS-TYR-TYR-LYS-ILE
J: CYS-TYR-TYR-LYS-ILE
K: CYS-TYR-TYR-LYS-ILE
L: CYS-TYR-TYR-LYS-ILE
M: CYS-TYR-TYR-LYS-ILE
N: CYS-TYR-TYR-LYS-ILE
O: CYS-TYR-TYR-LYS-ILE
P: CYS-TYR-TYR-LYS-ILE
Q: CYS-TYR-TYR-LYS-ILE
R: CYS-TYR-TYR-LYS-ILE


Theoretical massNumber of molelcules
Total (without water)284,90318
Polymers284,90318
Non-polymers00
Water00
1
A: Periplasmic serine endoprotease DegP
B: Periplasmic serine endoprotease DegP
C: Periplasmic serine endoprotease DegP
D: Periplasmic serine endoprotease DegP
E: Periplasmic serine endoprotease DegP
F: Periplasmic serine endoprotease DegP
G: CYS-TYR-TYR-LYS-ILE
H: CYS-TYR-TYR-LYS-ILE
I: CYS-TYR-TYR-LYS-ILE
J: CYS-TYR-TYR-LYS-ILE
K: CYS-TYR-TYR-LYS-ILE
L: CYS-TYR-TYR-LYS-ILE
M: CYS-TYR-TYR-LYS-ILE
N: CYS-TYR-TYR-LYS-ILE
O: CYS-TYR-TYR-LYS-ILE
P: CYS-TYR-TYR-LYS-ILE
Q: CYS-TYR-TYR-LYS-ILE
R: CYS-TYR-TYR-LYS-ILE

A: Periplasmic serine endoprotease DegP
B: Periplasmic serine endoprotease DegP
C: Periplasmic serine endoprotease DegP
D: Periplasmic serine endoprotease DegP
E: Periplasmic serine endoprotease DegP
F: Periplasmic serine endoprotease DegP
G: CYS-TYR-TYR-LYS-ILE
H: CYS-TYR-TYR-LYS-ILE
I: CYS-TYR-TYR-LYS-ILE
J: CYS-TYR-TYR-LYS-ILE
K: CYS-TYR-TYR-LYS-ILE
L: CYS-TYR-TYR-LYS-ILE
M: CYS-TYR-TYR-LYS-ILE
N: CYS-TYR-TYR-LYS-ILE
O: CYS-TYR-TYR-LYS-ILE
P: CYS-TYR-TYR-LYS-ILE
Q: CYS-TYR-TYR-LYS-ILE
R: CYS-TYR-TYR-LYS-ILE


Theoretical massNumber of molelcules
Total (without water)569,80636
Polymers569,80636
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)214.920, 122.427, 140.242
Angle α, β, γ (deg.)90.000, 117.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Periplasmic serine endoprotease DegP / Heat shock protein DegP / Protease Do


Mass: 46104.184 Da / Num. of mol.: 6 / Mutation: S210A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: degP, htrA, ptd, b0161, JW0157 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0V0, peptidase Do
#2: Protein/peptide
CYS-TYR-TYR-LYS-ILE


Mass: 689.843 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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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: 2.87 Å3/Da / Density % sol: 62.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 10% PEG3350 and 0.1 M tacsimate pH 3.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 37293 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 126.04 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.042 / Rrim(I) all: 0.11 / Χ2: 2.471 / Net I/σ(I): 11.2 / Num. measured all: 270801
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.6-3.667.50.52718150.9020.2060.5661.864100
3.66-3.737.50.56518850.9190.2220.6071.97899.9
3.73-3.87.40.54818560.940.2160.591.902100
3.8-3.887.40.42918480.9550.1680.4611.877100
3.88-3.967.40.43418570.9570.1710.4671.944100
3.96-4.057.40.3318470.9730.130.3552.02100
4.05-4.167.40.2818680.9770.1110.3012.046100
4.16-4.277.40.19318750.9890.0760.2082.277100
4.27-4.397.40.16218590.9880.0640.1742.589100
4.39-4.547.40.14118660.9920.0560.1522.386100
4.54-4.77.40.13118530.9910.0520.1412.37100
4.7-4.897.30.11818440.9930.0470.1272.32100
4.89-5.117.30.11118730.9930.0440.122.31100
5.11-5.387.20.10518920.9940.0420.1132.338100
5.38-5.716.90.10418410.9940.0430.1132.39100
5.71-6.157.50.09218860.9960.0360.0982.535100
6.15-6.777.50.07618700.9960.030.0822.929100
6.77-7.757.30.06718890.9970.0270.0723.392100
7.75-9.756.80.05818900.9970.0240.0634.038100
9.75-505.90.05818790.9960.0260.0644.48297.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OTP

3otp


Resolution: 3.6→35.479 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.05
RfactorNum. reflection% reflection
Rfree0.2653 1843 4.96 %
Rwork0.1993 --
obs0.2027 37191 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 236 Å2 / Biso mean: 136.6854 Å2 / Biso min: 61.26 Å2
Refinement stepCycle: final / Resolution: 3.6→35.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16997 0 0 0 16997
Num. residues----2368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5972-3.69440.37621200.3092543266393
3.6944-3.8030.43221340.3252726286099
3.803-3.92560.34981230.29162712283599
3.9256-4.06570.39491560.27842687284399
4.0657-4.22820.31071520.239327412893100
4.2282-4.42030.2711670.203127232890100
4.4203-4.65290.24461520.192126932845100
4.6529-4.94370.27881580.193627242882100
4.9437-5.32420.25021440.190627462890100
5.3242-5.85780.29541340.211927512885100
5.8578-6.70050.26571350.207627432878100
6.7005-8.42330.23671310.189427812912100
8.4233-35.48040.20081370.1382778291598

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