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- PDB-9fsw: ClpP from Staphylococcus epidermidis with glycerol in some of the... -

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Basic information

Entry
Database: PDB / ID: 9fsw
TitleClpP from Staphylococcus epidermidis with glycerol in some of the catalytic sites.
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / serine protease / peptidase / bacterial ClpP
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / identical protein binding / cytoplasm
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsAlves Franca, B. / Rohde, H. / Betzel, C.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)3907159 Germany
German Federal Ministry for Education and Research05K19GU4 Germany
German Federal Ministry for Education and Research05K20GUB Germany
CitationJournal: Sci Rep / Year: 2024
Title: Molecular insights into the dynamic modulation of bacterial ClpP function and oligomerization by peptidomimetic boronate compounds.
Authors: Alves Franca, B. / Falke, S. / Rohde, H. / Betzel, C.
History
DepositionJun 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,06038
Polymers309,48414
Non-polymers2,57524
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58360 Å2
ΔGint-429 kcal/mol
Surface area85840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.606, 123.989, 126.688
Angle α, β, γ (deg.)90.000, 91.184, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp


Mass: 22106.025 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria)
Gene: clpP, E1M97_03460, E1M98_06460, E1N00_07180, E1N03_05195, E1N04_00635, E1N05_04945, E1N06_06240, E1N09_07235, E1N11_03825, E1N12_01760, E1N13_04220, FHG76_01330, FHQ17_10195, H3963_07430, I3V53_07130
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N1MQL5, endopeptidase Clp
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M sodium acetate (NaOAc), 30 - 40% v/v MPD, and 0.01 - 0.04 M calcium chloride (CaCl2).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.83 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83 Å / Relative weight: 1
ReflectionResolution: 1.994→88.603 Å / Num. obs: 148087 / % possible obs: 75.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 44.94 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.046 / Rrim(I) all: 0.117 / Net I/σ(I): 9.4 / Num. measured all: 943499
Reflection shellResolution: 1.994→2.157 Å / % possible obs: 17.8 % / Redundancy: 7 % / Rmerge(I) obs: 1.303 / Num. measured all: 51337 / Num. unique obs: 7294 / Rpim(I) all: 0.529 / Rrim(I) all: 1.408 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→63.33 Å / SU ML: 0.3088 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.008
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2329 5721 4.99 %
Rwork0.1992 109001 -
obs0.2009 114722 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.34 Å2
Refinement stepCycle: LAST / Resolution: 2.39→63.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19327 0 172 562 20061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004219725
X-RAY DIFFRACTIONf_angle_d0.732426634
X-RAY DIFFRACTIONf_chiral_restr0.04633091
X-RAY DIFFRACTIONf_plane_restr0.00483458
X-RAY DIFFRACTIONf_dihedral_angle_d16.03987386
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.494976405386
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.588553467681
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.579962128765
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.547199951819
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.542492814256
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.648621335429
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS0.527614089078
ens_1d_9AAX-RAY DIFFRACTIONTorsion NCS0.572830023469
ens_1d_10AAX-RAY DIFFRACTIONTorsion NCS0.534759834499
ens_1d_11AAX-RAY DIFFRACTIONTorsion NCS0.571829751967
ens_1d_12AAX-RAY DIFFRACTIONTorsion NCS0.540975688279
ens_1d_13AAX-RAY DIFFRACTIONTorsion NCS0.590122241119
ens_1d_14AAX-RAY DIFFRACTIONTorsion NCS0.546608349197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.410.33152130.26943532X-RAY DIFFRACTION99.92
2.41-2.440.3331920.26543641X-RAY DIFFRACTION99.95
2.44-2.470.3411760.25643649X-RAY DIFFRACTION99.97
2.47-2.50.26971840.23063595X-RAY DIFFRACTION100
2.5-2.540.291760.23083654X-RAY DIFFRACTION99.97
2.54-2.570.30621910.22653624X-RAY DIFFRACTION100
2.57-2.610.29131650.22053663X-RAY DIFFRACTION100
2.61-2.650.26391840.2223644X-RAY DIFFRACTION100
2.65-2.690.28191850.21753651X-RAY DIFFRACTION99.95
2.69-2.730.29871800.21943614X-RAY DIFFRACTION100
2.73-2.780.26781730.20963608X-RAY DIFFRACTION99.97
2.78-2.830.27442000.21933627X-RAY DIFFRACTION100
2.83-2.880.26911820.21953651X-RAY DIFFRACTION100
2.88-2.940.28062130.22553623X-RAY DIFFRACTION99.95
2.94-3.010.28741830.23253619X-RAY DIFFRACTION100
3.01-3.080.24882040.23283578X-RAY DIFFRACTION100
3.08-3.150.32522150.23063617X-RAY DIFFRACTION100
3.15-3.240.24851820.21153668X-RAY DIFFRACTION99.95
3.24-3.330.22742110.21153588X-RAY DIFFRACTION99.84
3.33-3.440.24942350.20543604X-RAY DIFFRACTION99.77
3.44-3.570.25261650.19343628X-RAY DIFFRACTION99.89
3.57-3.710.24141880.20373647X-RAY DIFFRACTION99.92
3.71-3.880.23721710.20193676X-RAY DIFFRACTION99.95
3.88-4.080.22532000.18113628X-RAY DIFFRACTION99.84
4.08-4.340.21241920.1743641X-RAY DIFFRACTION99.9
4.34-4.670.17812280.16153603X-RAY DIFFRACTION99.92
4.67-5.140.21831860.18723632X-RAY DIFFRACTION99.74
5.14-5.880.24121770.21573699X-RAY DIFFRACTION99.79
5.88-7.410.19941600.20643691X-RAY DIFFRACTION99.84
7.41-63.330.15682100.15353706X-RAY DIFFRACTION99.37

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