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- PDB-9irm: Structure of ClpP from Staphylococcus aureus in complex with ZG283 -

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Basic information

Entry
Database: PDB / ID: 9irm
TitleStructure of ClpP from Staphylococcus aureus in complex with ZG283
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / ClpP / Staphylococcus aureus / activator / protease
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsWei, B.Y. / Wang, P.Y. / 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: Cell Rep Med / Year: 2024
Title: Structure-guided development of selective caseinolytic protease P agonists as antistaphylococcal agents.
Authors: Zhang, T. / Wang, P. / Zhou, H. / Wei, B. / Zhao, Y. / Li, J. / Zhang, M. / Wu, W. / Lan, L. / Gan, J. / Yang, C.G.
History
DepositionJul 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: 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

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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)311,36344
Polymers301,51114
Non-polymers9,85230
Water26,7881487
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58730 Å2
ΔGint-432 kcal/mol
Surface area88140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.410, 127.080, 146.100
Angle α, β, γ (deg.)90.00, 95.38, 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: 21536.531 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D1I3W4, endopeptidase Clp
#2: Chemical
ChemComp-WBW / (6S,9aS)-8-(anthracen-9-ylmethyl)-6-[(2S)-butan-2-yl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide


Mass: 568.630 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C31H35F3N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1487 / 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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 35% 2-Methyl-2,4-pentanediol, 0.1 M HEPES/Sodium hydroxide, pH 7.5, 0.2 M Sodium chloride

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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: Nov 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.81→31.89 Å / Num. obs: 314521 / % possible obs: 97.6 % / Redundancy: 5.3 % / CC1/2: 0.998 / Net I/σ(I): 11.1
Reflection shellResolution: 1.81→1.86 Å / Num. unique obs: 23142 / CC1/2: 0.643

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→31.89 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.793 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22614 15697 5 %RANDOM
Rwork0.21155 ---
obs0.21228 298790 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.257 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å2-0.01 Å2
2---0.58 Å20 Å2
3----0.66 Å2
Refinement stepCycle: 1 / Resolution: 1.81→31.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19418 0 702 1488 21608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01920479
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219289
X-RAY DIFFRACTIONr_angle_refined_deg1.1282.01127817
X-RAY DIFFRACTIONr_angle_other_deg0.835344624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16952569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68625.307831
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.337153417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1311597
X-RAY DIFFRACTIONr_chiral_restr0.1060.23262
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0222628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023763
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_it0.4422.72810308
X-RAY DIFFRACTIONr_mcbond_other0.4422.72810307
X-RAY DIFFRACTIONr_mcangle_it0.8064.07912843
X-RAY DIFFRACTIONr_mcangle_other0.8064.0812844
X-RAY DIFFRACTIONr_scbond_it0.382.8910171
X-RAY DIFFRACTIONr_scbond_other0.382.8910172
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6694.32214967
X-RAY DIFFRACTIONr_long_range_B_refined2.67433.64923679
X-RAY DIFFRACTIONr_long_range_B_other2.46933.34523242
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 1114 -
Rwork0.295 21974 -
obs--99.96 %

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