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

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Basic information

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


peptidase Do / programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / peptidase activity / response to heat / outer membrane-bounded periplasmic space ...peptidase Do / programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / peptidase activity / response to heat / outer membrane-bounded periplasmic space / response to oxidative stress / periplasmic space / positive regulation of apoptotic process / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 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 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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-ARG-LYS-LEU
M: CYS-TYR-ARG-LYS-LEU
H: CYS-TYR-ARG-LYS-LEU
N: CYS-TYR-ARG-LYS-LEU
I: CYS-TYR-ARG-LYS-LEU
Q: CYS-TYR-ARG-LYS-LEU
J: CYS-TYR-ARG-LYS-LEU
O: CYS-TYR-ARG-LYS-LEU
K: CYS-TYR-ARG-LYS-LEU
R: CYS-TYR-ARG-LYS-LEU
L: CYS-TYR-ARG-LYS-LEU
P: CYS-TYR-ARG-LYS-LEU


Theoretical massNumber of molelcules
Total (without water)284,83118
Polymers284,83118
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-ARG-LYS-LEU
M: CYS-TYR-ARG-LYS-LEU
H: CYS-TYR-ARG-LYS-LEU
N: CYS-TYR-ARG-LYS-LEU
I: CYS-TYR-ARG-LYS-LEU
Q: CYS-TYR-ARG-LYS-LEU
J: CYS-TYR-ARG-LYS-LEU
O: CYS-TYR-ARG-LYS-LEU
K: CYS-TYR-ARG-LYS-LEU
R: CYS-TYR-ARG-LYS-LEU
L: CYS-TYR-ARG-LYS-LEU
P: CYS-TYR-ARG-LYS-LEU

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-ARG-LYS-LEU
M: CYS-TYR-ARG-LYS-LEU
H: CYS-TYR-ARG-LYS-LEU
N: CYS-TYR-ARG-LYS-LEU
I: CYS-TYR-ARG-LYS-LEU
Q: CYS-TYR-ARG-LYS-LEU
J: CYS-TYR-ARG-LYS-LEU
O: CYS-TYR-ARG-LYS-LEU
K: CYS-TYR-ARG-LYS-LEU
R: CYS-TYR-ARG-LYS-LEU
L: CYS-TYR-ARG-LYS-LEU
P: CYS-TYR-ARG-LYS-LEU


Theoretical massNumber of molelcules
Total (without water)569,66336
Polymers569,66336
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)217.152, 123.519, 140.560
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: 46104.184 Da / Num. of mol.: 6
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-ARG-LYS-LEU


Mass: 683.863 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria)

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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: 2.92 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 11% PEG3350, 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 % / 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
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OTP
Resolution: 4.2→50 Å / Cor.coef. Fo:Fc: 0.852 / Cor.coef. Fo:Fc free: 0.753 / SU B: 71.699 / SU ML: 0.946 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.191
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3255 1262 5.1 %RANDOM
Rwork0.2477 ---
obs0.2516 23246 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 219.4 Å2 / Biso mean: 51.451 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å20.06 Å2
2--0.83 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 4.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17212 0 0 0 17212
Num. residues----2370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01917346
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217535
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.97623401
X-RAY DIFFRACTIONr_angle_other_deg1.943340245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03652341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.43226.692656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.983153103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4271566
X-RAY DIFFRACTIONr_chiral_restr0.0430.22815
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023525
LS refinement shellResolution: 4.157→4.265 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 81 -
Rwork0.27 1470 -
all-1551 -
obs--84.48 %

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