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- PDB-8szn: Crystal structure of Neisseria meningitidis ClpP protease in comp... -

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Basic information

Entry
Database: PDB / ID: 8szn
TitleCrystal structure of Neisseria meningitidis ClpP protease in complex with phosphine oxide compound ACP6-12
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / ClpP / protease / antibiotic / proteostasis / activator
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 speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsMabanglo, M.F. / Houry, W.A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-148564 Canada
CitationJournal: J.Med.Chem. / Year: 2024
Title: Structure-Based Design and Development of Phosphine Oxides as a Novel Chemotype for Antibiotics that Dysregulate Bacterial ClpP Proteases.
Authors: Lin, F. / Mabanglo, M.F. / Zhou, J.L. / Binepal, G. / Barghash, M.M. / Wong, K.S. / Gray-Owen, S.D. / Batey, R.A. / Houry, W.A.
History
DepositionMay 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: ATP-dependent Clp protease proteolytic subunit
W: ATP-dependent Clp protease proteolytic subunit
X: ATP-dependent Clp protease proteolytic subunit
Y: ATP-dependent Clp protease proteolytic subunit
Z: ATP-dependent Clp protease proteolytic subunit
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit
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)484,25432
Polymers477,32921
Non-polymers6,92411
Water8,683482
1
V: ATP-dependent Clp protease proteolytic subunit
W: ATP-dependent Clp protease proteolytic subunit
X: ATP-dependent Clp protease proteolytic subunit
Y: ATP-dependent Clp protease proteolytic subunit
Z: ATP-dependent Clp protease proteolytic subunit
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit
hetero molecules

V: ATP-dependent Clp protease proteolytic subunit
W: ATP-dependent Clp protease proteolytic subunit
X: ATP-dependent Clp protease proteolytic subunit
Y: ATP-dependent Clp protease proteolytic subunit
Z: ATP-dependent Clp protease proteolytic subunit
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,77326
Polymers318,22014
Non-polymers7,55412
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area57330 Å2
ΔGint-234 kcal/mol
Surface area97130 Å2
MethodPISA
2
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)321,36719
Polymers318,22014
Non-polymers3,1475
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55550 Å2
ΔGint-228 kcal/mol
Surface area93940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.800, 357.780, 180.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Components on special symmetry positions
IDModelComponents
11Z-420-

HOH

21Z-421-

HOH

31G-324-

HOH

41N-404-

HOH

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Components

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


Mass: 22729.967 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: clpP, NMB1312 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JZ38, endopeptidase Clp
#2: Chemical
ChemComp-X3O / 2-{bis[5-(trifluoromethyl)pyridin-2-yl]phosphoryl}-2-methyl-N-(2-{[2-(trifluoromethyl)phenyl]sulfanyl}ethyl)propanamide


Mass: 629.478 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C25H21F9N3O2PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate; 40% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.33→48.85 Å / Num. obs: 209451 / % possible obs: 98.79 % / Redundancy: 13.4 % / Biso Wilson estimate: 65.23 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1622 / Rpim(I) all: 0.04587 / Rrim(I) all: 0.1687 / Net I/σ(I): 11.03
Reflection shellResolution: 2.33→2.41 Å / Num. unique obs: 20763 / CC1/2: 0.123 / CC star: 0.467

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→48.85 Å / SU ML: 0.4427 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.8356
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2816 10359 5 %
Rwork0.2218 196638 -
obs0.2248 206997 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.45 Å2
Refinement stepCycle: LAST / Resolution: 2.33→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30194 0 451 482 31127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008831087
X-RAY DIFFRACTIONf_angle_d1.064141925
X-RAY DIFFRACTIONf_chiral_restr0.05494690
X-RAY DIFFRACTIONf_plane_restr0.01345424
X-RAY DIFFRACTIONf_dihedral_angle_d17.924311745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.360.39472750.36735143X-RAY DIFFRACTION78.68
2.36-2.380.38653270.35245988X-RAY DIFFRACTION90.98
2.38-2.410.37243310.33056366X-RAY DIFFRACTION96.3
2.41-2.440.36853380.33296495X-RAY DIFFRACTION99.2
2.44-2.480.38643460.3316563X-RAY DIFFRACTION99.48
2.48-2.510.40013450.32576550X-RAY DIFFRACTION99.7
2.51-2.550.37253490.31616617X-RAY DIFFRACTION99.91
2.55-2.580.37313450.32136566X-RAY DIFFRACTION99.96
2.58-2.620.37893480.32296615X-RAY DIFFRACTION99.97
2.62-2.670.35383470.33486586X-RAY DIFFRACTION99.96
2.67-2.710.41043470.32126588X-RAY DIFFRACTION99.99
2.71-2.760.36393460.30656578X-RAY DIFFRACTION99.99
2.76-2.820.40483490.29316630X-RAY DIFFRACTION100
2.82-2.870.3373460.27366580X-RAY DIFFRACTION100
2.87-2.940.33413480.25266614X-RAY DIFFRACTION100
2.94-30.33623490.25356614X-RAY DIFFRACTION99.96
3-3.080.31263480.25126619X-RAY DIFFRACTION99.99
3.08-3.160.31343480.25916607X-RAY DIFFRACTION100
3.16-3.260.32213490.26426630X-RAY DIFFRACTION99.99
3.26-3.360.3213480.24926618X-RAY DIFFRACTION100
3.36-3.480.3233490.2426641X-RAY DIFFRACTION100
3.48-3.620.3033490.22036621X-RAY DIFFRACTION100
3.62-3.780.2833490.22266632X-RAY DIFFRACTION99.97
3.78-3.980.27683510.2056669X-RAY DIFFRACTION100
3.98-4.230.2483520.17826682X-RAY DIFFRACTION99.94
4.23-4.560.22783510.16736667X-RAY DIFFRACTION100
4.56-5.020.25033520.17666701X-RAY DIFFRACTION99.99
5.02-5.740.28323530.21466709X-RAY DIFFRACTION100
5.74-7.230.28533580.2146788X-RAY DIFFRACTION99.99
7.23-48.850.17943660.1746961X-RAY DIFFRACTION99.81

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