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

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Basic information

Entry
Database: PDB / ID: 6jjo
TitleCrystal structure of the DegP dodecamer with a modulator
Components
  • Periplasmic serine endoprotease DegP
  • TMB-CYRKL modulator
KeywordsHYDROLASE / Protease
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: 4.157 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: TMB-CYRKL modulator
M: TMB-CYRKL modulator
H: TMB-CYRKL modulator
N: TMB-CYRKL modulator
I: TMB-CYRKL modulator
O: TMB-CYRKL modulator
J: TMB-CYRKL modulator
P: TMB-CYRKL modulator
K: TMB-CYRKL modulator
Q: TMB-CYRKL modulator
L: TMB-CYRKL modulator
R: TMB-CYRKL modulator


Theoretical massNumber of molelcules
Total (without water)303,13918
Polymers303,13918
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: TMB-CYRKL modulator
M: TMB-CYRKL modulator
H: TMB-CYRKL modulator
N: TMB-CYRKL modulator
I: TMB-CYRKL modulator
O: TMB-CYRKL modulator
J: TMB-CYRKL modulator
P: TMB-CYRKL modulator
K: TMB-CYRKL modulator
Q: TMB-CYRKL modulator
L: TMB-CYRKL modulator
R: TMB-CYRKL modulator

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: TMB-CYRKL modulator
M: TMB-CYRKL modulator
H: TMB-CYRKL modulator
N: TMB-CYRKL modulator
I: TMB-CYRKL modulator
O: TMB-CYRKL modulator
J: TMB-CYRKL modulator
P: TMB-CYRKL modulator
K: TMB-CYRKL modulator
Q: TMB-CYRKL modulator
L: TMB-CYRKL modulator
R: TMB-CYRKL modulator


Theoretical massNumber of molelcules
Total (without water)606,27836
Polymers606,27836
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)217.148, 123.518, 140.558
Angle α, β, γ (deg.)90.000, 118.000, 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: 49155.473 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
TMB-CYRKL modulator


Mass: 683.863 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: 2.75 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 11% PEG3350 and 0.1 M tacsimate pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. obs: 24531 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 151.78 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.045 / Rrim(I) all: 0.121 / Χ2: 1.944 / Net I/σ(I): 9.1 / Num. measured all: 176600
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.2-4.277.10.66512270.9210.2690.7181.776100
4.27-4.357.10.48412140.9530.1940.5221.908100
4.35-4.4370.4412070.920.180.4762.014100
4.43-4.527.20.4112290.9450.1640.4421.9100
4.52-4.627.20.39812210.9590.1590.4291.868100
4.62-4.737.20.36112040.9560.1450.391.77299.9
4.73-4.857.20.31312590.9760.1250.3371.742100
4.85-4.987.20.3112030.9730.1240.3341.725100
4.98-5.137.20.29212110.9820.1170.3151.662100
5.13-5.297.10.28412280.980.1140.3061.733100
5.29-5.4870.28212420.9780.1150.3041.691100
5.48-5.76.70.28312170.9690.1190.3081.771100
5.7-5.967.40.24812270.9870.0980.2671.771100
5.96-6.277.60.18412310.990.0720.1981.813100
6.27-6.667.60.14312270.9950.0560.1531.878100
6.66-7.187.50.10712280.9960.0420.1151.943100
7.18-7.97.50.08312340.9970.0330.0891.979100
7.9-9.037.50.05512430.9980.0210.0592.083100
9.03-11.367.30.04812490.9980.0190.0512.471100
11.36-506.40.05612300.9950.0240.0613.55396.9

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Processing

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

3otp


Resolution: 4.157→35.61 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 1262 5.16 %
Rwork0.2158 23174 -
obs0.2191 24436 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 325.25 Å2 / Biso mean: 174.9717 Å2 / Biso min: 94.59 Å2
Refinement stepCycle: final / Resolution: 4.157→35.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16906 0 0 0 16906
Num. residues----2370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.157-4.32310.33131230.27842290241389
4.3231-4.51950.30891360.255826062742100
4.5195-4.75730.3661180.253626132731100
4.7573-5.05450.33521510.247325942745100
5.0545-5.44350.2891240.244826402764100
5.4435-5.9890.36761270.262326022729100
5.989-6.85030.29261830.248825792762100
6.8503-8.61040.26341490.218726162765100
8.6104-35.61170.2221510.15722634278598

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