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- PDB-9k2d: Structure of ClpP from Staphylococcus aureus in complex with ZY39 -

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Basic information

Entry
Database: PDB / ID: 9k2d
TitleStructure of ClpP from Staphylococcus aureus in complex with ZY39
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsANTIBIOTIC / ClpP / Staphylococcus aureus / activator / protease / HYDROLASE
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 / 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 aureus subsp. aureus Mu3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsWei, B.Y. / Wang, P.Y. / Wu, W. / Zhang, T. / Yang, C.-G.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22037007 China
National Natural Science Foundation of China (NSFC)22107109 China
National Natural Science Foundation of China (NSFC)22307029 China
CitationJournal: J.Med.Chem. / Year: 2025
Title: Structure-Guided Development of ClpP Agonists with Potent Therapeutic Activities against Staphylococcus aureus Infection.
Authors: Zhang, T. / Wu, W. / Zhao, Y. / Ding, Z. / Wei, B. / Yang, T. / Li, J. / Wang, P. / Lan, L. / Gan, J. / Yang, C.G.
History
DepositionOct 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 19, 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)322,45142
Polymers313,11614
Non-polymers9,33528
Water21,6541202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58570 Å2
ΔGint-415 kcal/mol
Surface area91110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.659, 190.444, 96.562
Angle α, β, γ (deg.)90.00, 117.40, 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: 22365.414 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu3 (bacteria)
Gene: clpP, SAHV_0765 / Production host: Escherichia coli (E. coli) / References: UniProt: A7WZR9, endopeptidase Clp
#2: Chemical
ChemComp-A1EEK / (6~{S},9~{a}~{S})-6-[(2~{S})-butan-2-yl]-8-[(4-methoxynaphthalen-1-yl)methyl]-4,7-bis(oxidanylidene)-~{N}-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9~{a}-tetrahydro-2~{H}-pyrazino[1,2-a]pyrimidine-1-carboxamide


Mass: 548.597 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C28H35F3N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 35%(w/v) 2-methyl-2,4-pentanediol (MDP), 100 mM MES/NaOH (pH = 6.0), 200 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→95.22 Å / Num. obs: 266038 / % possible obs: 98.8 % / Redundancy: 5.9 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.045 / Rrim(I) all: 0.115 / Χ2: 1.567 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.975.30.714261730.7330.920.3330.790.53797.5
1.97-2.055.60.562263460.8360.9540.2510.6170.66598.2
2.05-2.145.60.427262850.9020.9740.1910.4690.80798
2.14-2.255.60.324263740.9430.9850.1450.3561.01298.1
2.25-2.395.80.252264510.9650.9910.1110.2761.21198.7
2.39-2.5860.199266780.9770.9940.0860.2171.41399.3
2.58-2.8460.154266930.9850.9960.0670.1691.74599.1
2.84-3.256.40.119268630.990.9970.050.1292.20599.8
3.25-4.096.50.088269590.9940.9990.0370.0952.76499.9
4.09-306.70.066272160.9960.9990.0280.0722.59999.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→95.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.245 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 9831 4.9 %RANDOM
Rwork0.20771 ---
obs0.20873 192103 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20.64 Å2
2---2.02 Å2-0 Å2
3---1.04 Å2
Refinement stepCycle: 1 / Resolution: 1.98→95.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19754 0 658 1202 21614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01920743
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219587
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.97228135
X-RAY DIFFRACTIONr_angle_other_deg0.832345397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39952587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80225.446874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.902153545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.18915101
X-RAY DIFFRACTIONr_chiral_restr0.0560.23282
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0223799
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023770
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5513.29510385
X-RAY DIFFRACTIONr_mcbond_other0.553.29510384
X-RAY DIFFRACTIONr_mcangle_it0.9744.93112954
X-RAY DIFFRACTIONr_mcangle_other0.9744.93112941
X-RAY DIFFRACTIONr_scbond_it0.523.39110358
X-RAY DIFFRACTIONr_scbond_other0.523.39110359
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9055.06515175
X-RAY DIFFRACTIONr_long_range_B_refined2.55940.11723001
X-RAY DIFFRACTIONr_long_range_B_other2.38639.89922732
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.982→2.033 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 707 -
Rwork0.278 13745 -
obs--93.38 %

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