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- PDB-8r05: Photorhabdus lamondii ClpP in complex with the natural product be... -

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Basic information

Entry
Database: PDB / ID: 8r05
TitlePhotorhabdus lamondii ClpP in complex with the natural product beta-lactone inhibitor Cystargolide A at 2.5 A resolution
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / anti-virulence / caseinolytic protease / inhibitor / natural product / mode of action
Function / homology
Function and homology information


endopeptidase Clp / ATP-dependent peptidase activity / serine-type endopeptidase activity / proteolysis / 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
Cystargolide A (bound) / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesPhotorhabdus laumondii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsIlligmann, A. / Vielberg, M.-T. / Lakemeyer, M. / Wolf, F. / Staudt, N. / Dema, T. / Stange, P. / Liebhart, E. / Kuttenlochner, W. / Kulik, A. ...Illigmann, A. / Vielberg, M.-T. / Lakemeyer, M. / Wolf, F. / Staudt, N. / Dema, T. / Stange, P. / Liebhart, E. / Kuttenlochner, W. / Kulik, A. / Malik, I. / Grond, S. / Sieber, S.A. / Groll, M. / Kaysser, L. / Broetz-Oesterhelt, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/10-3 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Structure of Staphylococcus aureus ClpP Bound to the Covalent Active-Site Inhibitor Cystargolide A.
Authors: Illigmann, A. / Vielberg, M.T. / Lakemeyer, M. / Wolf, F. / Dema, T. / Stange, P. / Kuttenlochner, W. / Liebhart, E. / Kulik, A. / Staudt, N.D. / Malik, I. / Grond, S. / Sieber, S.A. / ...Authors: Illigmann, A. / Vielberg, M.T. / Lakemeyer, M. / Wolf, F. / Dema, T. / Stange, P. / Kuttenlochner, W. / Liebhart, E. / Kulik, A. / Staudt, N.D. / Malik, I. / Grond, S. / Sieber, S.A. / Kaysser, L. / Groll, M. / Brotz-Oesterhelt, H.
History
DepositionOct 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)331,88828
Polymers326,67314
Non-polymers5,21414
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58640 Å2
ΔGint-242 kcal/mol
Surface area92330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.070, 177.940, 102.840
Angle α, β, γ (deg.)90.00, 112.16, 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: 23333.803 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus laumondii (bacteria) / Gene: clpP, plu3869 / Plasmid: pET-Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7N0L3, endopeptidase Clp
#2: Chemical
ChemComp-VSZ / Cystargolide A (bound) / (2S,3S)-2-[[(2S)-2-[[(2R,3S)-3-methanoyl-4-methyl-2-oxidanyl-pentanoyl]amino]-3-methyl-butanoyl]amino]-3-methyl-pentanoic acid


Mass: 372.456 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C18H32N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 20% PEG 4000, 10% isopropanole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 107872 / % possible obs: 97.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.9
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2 / Num. unique obs: 11693 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 24.62 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23413 5391 5 %RANDOM
Rwork0.18652 ---
obs0.18888 102428 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.965 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å21.58 Å2
2---3.77 Å20 Å2
3---2.21 Å2
Refinement stepCycle: 1 / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20456 0 0 101 20557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01320780
X-RAY DIFFRACTIONr_bond_other_d0.0010.01520388
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.64327996
X-RAY DIFFRACTIONr_angle_other_deg1.0411.57846932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84252547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.9222.161051
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.911153788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.20315129
X-RAY DIFFRACTIONr_chiral_restr0.0380.22855
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0223064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024470
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_it2.295.01410266
X-RAY DIFFRACTIONr_mcbond_other2.295.01410265
X-RAY DIFFRACTIONr_mcangle_it3.1897.51212787
X-RAY DIFFRACTIONr_mcangle_other3.1897.51212788
X-RAY DIFFRACTIONr_scbond_it2.2575.4610514
X-RAY DIFFRACTIONr_scbond_other2.2565.4610515
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1488.04715210
X-RAY DIFFRACTIONr_long_range_B_refined4.21658.69321214
X-RAY DIFFRACTIONr_long_range_B_other4.19858.68221207
X-RAY DIFFRACTIONr_rigid_bond_restr0.509341168
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 387 -
Rwork0.303 7357 -
obs--95.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.17310.10620.0240.24370.04380.1396-0.00450.0683-0.0818-0.0315-0.0028-0.07240.0370.04730.00730.0744-0.00180.06280.0972-0.06770.11455.6694.92251.172
20.24250.22180.02920.32420.21420.8158-0.0117-0.0378-0.1163-0.0174-0.0181-0.08570.0284-0.00260.02980.05930.01620.02750.01910.00370.170457.44984.93675.491
30.18730.03620.00330.38240.14580.2096-0.0034-0.0712-0.1156-0.0219-0.0133-0.0215-0.0157-0.02410.01670.06790.00810.00470.03590.03820.144937.19482.62992.584
40.2538-0.06340.10050.57430.19280.13350.0141-0.0478-0.0583-0.02310.00030.0173-0.005-0.0199-0.01430.0816-0.01120.02680.06530.03010.097812.05990.86589.688
50.2416-0.0073-0.00850.60930.02370.1359-0.01320.0431-0.0626-0.00330.00750.0445-0.01960.00730.00570.0682-0.00840.0070.0892-0.01180.0860.76103.56469.054
60.4640.1781-0.0560.7536-0.03420.0095-0.04330.1511-0.006-0.05120.04330.02070.0204-0.01280.00010.0966-0.0109-0.00170.1456-0.01850.003511.695110.7446.217
70.36360.24380.0780.53890.05250.0203-0.02520.2026-0.0629-0.0260.0397-0.0520.00260.0459-0.01450.0947-0.02930.04060.1651-0.04450.027536.802107.23938.596
80.3968-0.0145-0.04860.50040.0680.01940.0078-0.13960.04950.02690.004-0.04150.01780.024-0.01170.0695-0.0033-0.02470.1432-0.02260.0450.891123.094110.59
90.1952-0.0337-0.1810.29630.07830.24290.0037-0.04080.04690.003-0.0106-0.05960.00170.03250.00690.0290.0039-0.01490.0861-0.02730.131768.9126.91791.829
100.11290.08290.02660.2480.13990.2442-0.01280.04060.0808-0.02580.0005-0.0506-0.00210.0030.01240.0436-0.02060.01770.07070.01260.177666.578139.02769.288
110.41640.05790.11890.31610.16410.2294-0.02330.07550.1683-0.04030.0054-0.05690.0097-0.01440.01790.0696-0.01420.01730.04790.0620.136245.966149.07956.708
120.31120.15090.02620.41150.0370.1253-0.02490.02060.0933-0.0224-0.004-0.0067-0.0014-0.02940.02890.0782-0.0003-0.00390.04120.03760.126221.561151.24466.864
130.17370.23650.10470.7703-0.05870.2085-0.0185-0.03630.04970.0180.01870.02050.0034-0.0326-0.00020.06010.02950.01280.0659-0.02880.131612.519142.96890.282
140.37760.02340.10810.5437-0.05830.06760.028-0.11440.03670.0648-0.01010.0194-0.00310.0213-0.01780.0657-0.00580.02270.1366-0.05670.038325.566130.278109.744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 206
2X-RAY DIFFRACTION2B17 - 205
3X-RAY DIFFRACTION3C16 - 206
4X-RAY DIFFRACTION4D17 - 206
5X-RAY DIFFRACTION5E17 - 206
6X-RAY DIFFRACTION6F17 - 206
7X-RAY DIFFRACTION7G16 - 206
8X-RAY DIFFRACTION8H17 - 206
9X-RAY DIFFRACTION9I15 - 206
10X-RAY DIFFRACTION10J17 - 206
11X-RAY DIFFRACTION11K17 - 206
12X-RAY DIFFRACTION12L17 - 207
13X-RAY DIFFRACTION13M17 - 206
14X-RAY DIFFRACTION14N17 - 206

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