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- PDB-8szm: Crystal structure of E. coli ClpP protease in complex with phosph... -

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Basic information

Entry
Database: PDB / ID: 8szm
TitleCrystal structure of E. coli ClpP protease in complex with phosphine oxide compound ACP6-12
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / ClpP / protease / activator / antibiotic / proteostasis
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / transferase activity / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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

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Assembly

Deposited unit
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
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
O: ATP-dependent Clp protease proteolytic subunit
P: ATP-dependent Clp protease proteolytic subunit
Q: ATP-dependent Clp protease proteolytic subunit
R: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
U: ATP-dependent Clp protease proteolytic subunit
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)651,84331
Polymers649,95428
Non-polymers1,8883
Water2,450136
1
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,60715
Polymers324,97714
Non-polymers6291
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54050 Å2
ΔGint-234 kcal/mol
Surface area90710 Å2
MethodPISA
2
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

O: ATP-dependent Clp protease proteolytic subunit
P: ATP-dependent Clp protease proteolytic subunit
Q: ATP-dependent Clp protease proteolytic subunit
R: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
U: ATP-dependent Clp protease proteolytic subunit


Theoretical massNumber of molelcules
Total (without water)326,23616
Polymers324,97714
Non-polymers1,2592
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area54360 Å2
ΔGint-231 kcal/mol
Surface area90550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.968, 187.589, 169.408
Angle α, β, γ (deg.)90.000, 93.720, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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


Mass: 23212.650 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: clpP, clpP_1, clpP_2, clpP_3, clpP_4 / Production host: Escherichia coli (E. coli) / References: UniProt: C3TLT2, 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.: 3 / Source method: obtained synthetically / Formula: C25H21F9N3O2PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
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 PILATUS3 S 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: 2.35→79.83 Å / Num. obs: 236844 / % possible obs: 97.23 % / Redundancy: 2 % / Biso Wilson estimate: 44 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.06853 / Rpim(I) all: 0.06853 / Rrim(I) all: 0.09691 / Net I/σ(I): 8.78
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 0.6187 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 23019 / CC1/2: 0.22 / Rpim(I) all: 0.6187 / Rrim(I) all: 0.8749

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→79.83 Å / SU ML: 0.4088 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3985
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2603 11827 4.99 %
Rwork0.2035 225016 -
obs0.2063 236843 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.77 Å2
Refinement stepCycle: LAST / Resolution: 2.35→79.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39363 0 123 136 39622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00840124
X-RAY DIFFRACTIONf_angle_d0.999554121
X-RAY DIFFRACTIONf_chiral_restr0.05356115
X-RAY DIFFRACTIONf_plane_restr0.00877022
X-RAY DIFFRACTIONf_dihedral_angle_d18.52715172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.370.35713700.33667231X-RAY DIFFRACTION94.14
2.37-2.40.38613920.3447323X-RAY DIFFRACTION95.34
2.4-2.430.37953850.32717362X-RAY DIFFRACTION96.03
2.43-2.460.38164100.31627403X-RAY DIFFRACTION95.99
2.46-2.490.38283800.31437339X-RAY DIFFRACTION95.97
2.49-2.530.3753940.30447519X-RAY DIFFRACTION96.32
2.53-2.560.35984030.29017296X-RAY DIFFRACTION96.21
2.56-2.60.34714060.28387450X-RAY DIFFRACTION96.39
2.6-2.640.31864040.26947358X-RAY DIFFRACTION96.61
2.64-2.690.33234380.25727498X-RAY DIFFRACTION96.57
2.69-2.730.33253970.26677363X-RAY DIFFRACTION96.7
2.73-2.780.30744290.25757426X-RAY DIFFRACTION96.86
2.78-2.840.31774270.23937456X-RAY DIFFRACTION97.08
2.84-2.890.31444100.24257457X-RAY DIFFRACTION97.18
2.89-2.960.31113850.22117502X-RAY DIFFRACTION97.18
2.96-3.030.29544070.22667535X-RAY DIFFRACTION97.35
3.03-3.10.2853800.21347436X-RAY DIFFRACTION97.44
3.1-3.190.28823810.21317548X-RAY DIFFRACTION97.58
3.19-3.280.30844010.21767577X-RAY DIFFRACTION97.78
3.28-3.380.28784010.21797523X-RAY DIFFRACTION97.75
3.38-3.510.28553460.22617562X-RAY DIFFRACTION97.55
3.51-3.650.2683940.20037497X-RAY DIFFRACTION97.26
3.65-3.810.23093570.1787633X-RAY DIFFRACTION98.41
3.81-4.010.23973800.16947647X-RAY DIFFRACTION98.43
4.01-4.260.2043850.16157660X-RAY DIFFRACTION98.69
4.26-4.590.19434090.1537611X-RAY DIFFRACTION98.74
4.59-5.060.21073930.167661X-RAY DIFFRACTION98.96
5.06-5.790.24233760.19577702X-RAY DIFFRACTION98.97
5.79-7.290.2193770.18167723X-RAY DIFFRACTION99
7.29-79.830.17514100.14397718X-RAY DIFFRACTION98.08

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