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- PDB-9g72: Crystal structure of S. epidermidis ClpP in complex with tavaboro... -

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Basic information

Entry
Database: PDB / ID: 9g72
TitleCrystal structure of S. epidermidis ClpP in complex with tavaborole - soaking
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Peptidase / ClpP / Proteolysis / Antibiotics
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
: / ACETATE ION / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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
DepositionJul 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)312,42442
Polymers309,48414
Non-polymers2,94028
Water24,4281356
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53400 Å2
ΔGint-217 kcal/mol
Surface area85330 Å2
Unit cell
Length a, b, c (Å)94.922, 123.522, 127.029
Angle α, β, γ (deg.)90.00, 91.47, 90.00
Int Tables number4
Space group name H-MP1211

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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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-A1II0 / 3-fluoranyl-7-oxidanyl-8-oxa-7$l^{4}-borabicyclo[4.3.0]nona-1(9),2,4,6-tetraene


Mass: 150.923 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C7H5BFO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1356 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M NaOAc (pH 4.5), 30 - 40% (v/v) MPD, and 30 - 40 mM 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: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.692→75.314 Å / Num. obs: 265537 / % possible obs: 81.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 13.9 / Num. measured all: 1859890
Reflection shellResolution: 1.692→1.803 Å / % possible obs: 23.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.25 / Num. measured all: 94558 / Num. unique obs: 13277 / Rpim(I) all: 0.495 / Rrim(I) all: 1.346 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→75.25 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 1989 0.89 %
Rwork0.1999 --
obs0.2 222946 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→75.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19096 0 210 1356 20662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_d1.151
X-RAY DIFFRACTIONf_dihedral_angle_d17.0037144
X-RAY DIFFRACTIONf_chiral_restr0.0893099
X-RAY DIFFRACTIONf_plane_restr0.0133429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.32091370.307815654X-RAY DIFFRACTION98
1.96-2.010.34221400.276715651X-RAY DIFFRACTION98
2.01-2.070.27381430.252615572X-RAY DIFFRACTION98
2.07-2.140.26341430.239915577X-RAY DIFFRACTION98
2.14-2.210.24341410.229715713X-RAY DIFFRACTION98
2.21-2.30.2181450.223215782X-RAY DIFFRACTION99
2.3-2.410.21411400.217115830X-RAY DIFFRACTION99
2.41-2.540.23041370.212415844X-RAY DIFFRACTION99
2.54-2.690.22721420.209815885X-RAY DIFFRACTION99
2.69-2.90.21071380.212915835X-RAY DIFFRACTION99
2.9-3.190.21441500.202315707X-RAY DIFFRACTION98
3.19-3.660.20171330.195715899X-RAY DIFFRACTION99
3.66-4.610.17451510.162115982X-RAY DIFFRACTION100
4.61-75.250.19461490.183916026X-RAY DIFFRACTION99

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