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- PDB-11mi: Crystal Structure of M. tuberculosis ClpP1P2 bound to ADEP 19 -

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Basic information

Entry
Database: PDB / ID: 11mi
TitleCrystal Structure of M. tuberculosis ClpP1P2 bound to ADEP 19
Components(ATP-dependent Clp protease proteolytic subunit ...) x 2
KeywordsANTIBIOTIC / peptidase / protease / mycobacteria / tuberculosis / acyldepsipeptide / proteostasis
Function / homology
Function and homology information


endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / proteolysis / plasma membrane / 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
: / BENZOIC ACID / LEUCINE / DI(HYDROXYETHYL)ETHER / ATP-dependent Clp protease proteolytic subunit 2 / ATP-dependent Clp protease proteolytic subunit 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsBurnside, C.M. / Fei, F. / Schmitz, K.R. / Sello, J.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI171196 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM133395 United States
Citation
Journal: J.Med.Chem. / Year: 2026
Title: Structural and Mechanistic Studies of ADEPs Yield Potent Antibacterials and a Drug Formulation Strategy for Tuberculosis.
Authors: Fei, F. / Burnside, C.M. / Lun, S. / Wee, D. / Kaur, M. / Anderson, H.R. / McCarroll, M.N. / Richardson, A.E. / Neglia, S. / Liu, H.M. / Wang, X. / Gupta, S. / Rhee, K.Y. / Wright, G.D. / ...Authors: Fei, F. / Burnside, C.M. / Lun, S. / Wee, D. / Kaur, M. / Anderson, H.R. / McCarroll, M.N. / Richardson, A.E. / Neglia, S. / Liu, H.M. / Wang, X. / Gupta, S. / Rhee, K.Y. / Wright, G.D. / Bryson, B.D. / Oehlers, S.H. / Bishai, W.R. / Schmitz, K.R. / Sello, J.K.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 4, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2026Provider: 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 2
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2
H: ATP-dependent Clp protease proteolytic subunit 1
I: ATP-dependent Clp protease proteolytic subunit 1
J: ATP-dependent Clp protease proteolytic subunit 1
K: ATP-dependent Clp protease proteolytic subunit 1
L: ATP-dependent Clp protease proteolytic subunit 1
M: ATP-dependent Clp protease proteolytic subunit 1
N: ATP-dependent Clp protease proteolytic subunit 1
O: ATP-dependent Clp protease proteolytic subunit 2
P: ATP-dependent Clp protease proteolytic subunit 2
Q: ATP-dependent Clp protease proteolytic subunit 2
R: ATP-dependent Clp protease proteolytic subunit 2
S: ATP-dependent Clp protease proteolytic subunit 2
T: ATP-dependent Clp protease proteolytic subunit 2
U: ATP-dependent Clp protease proteolytic subunit 2
V: ATP-dependent Clp protease proteolytic subunit 1
W: ATP-dependent Clp protease proteolytic subunit 1
X: ATP-dependent Clp protease proteolytic subunit 1
Y: ATP-dependent Clp protease proteolytic subunit 1
Z: ATP-dependent Clp protease proteolytic subunit 1
a: ATP-dependent Clp protease proteolytic subunit 1
b: ATP-dependent Clp protease proteolytic subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)648,734132
Polymers626,03628
Non-polymers22,698104
Water8,251458
1
A: ATP-dependent Clp protease proteolytic subunit 2
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2
H: ATP-dependent Clp protease proteolytic subunit 1
I: ATP-dependent Clp protease proteolytic subunit 1
J: ATP-dependent Clp protease proteolytic subunit 1
K: ATP-dependent Clp protease proteolytic subunit 1
L: ATP-dependent Clp protease proteolytic subunit 1
M: ATP-dependent Clp protease proteolytic subunit 1
N: ATP-dependent Clp protease proteolytic subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,36766
Polymers313,01814
Non-polymers11,34952
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61020 Å2
ΔGint-193 kcal/mol
Surface area90000 Å2
MethodPISA
2
O: ATP-dependent Clp protease proteolytic subunit 2
P: ATP-dependent Clp protease proteolytic subunit 2
Q: ATP-dependent Clp protease proteolytic subunit 2
R: ATP-dependent Clp protease proteolytic subunit 2
S: ATP-dependent Clp protease proteolytic subunit 2
T: ATP-dependent Clp protease proteolytic subunit 2
U: ATP-dependent Clp protease proteolytic subunit 2
V: ATP-dependent Clp protease proteolytic subunit 1
W: ATP-dependent Clp protease proteolytic subunit 1
X: ATP-dependent Clp protease proteolytic subunit 1
Y: ATP-dependent Clp protease proteolytic subunit 1
Z: ATP-dependent Clp protease proteolytic subunit 1
a: ATP-dependent Clp protease proteolytic subunit 1
b: ATP-dependent Clp protease proteolytic subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,36766
Polymers313,01814
Non-polymers11,34952
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59420 Å2
ΔGint-192 kcal/mol
Surface area90010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.461, 183.685, 191.698
Angle α, β, γ (deg.)90.000, 95.337, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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ATP-dependent Clp protease proteolytic subunit ... , 2 types, 28 molecules ABCDEFGOPQRSTUHIJKLMNVWXYZab

#1: Protein
ATP-dependent Clp protease proteolytic subunit 2 / Endopeptidase Clp 2


Mass: 23650.910 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: mature M. tuberculosis ClpP2 with a C-terminal 6xHis tag
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: clpP2, Rv2460c, MTV008.16c / Production host: Escherichia coli B (bacteria) / Strain (production host): ER2566 / Variant (production host): delta-clpP / References: UniProt: P9WPC3, endopeptidase Clp
#2: Protein
ATP-dependent Clp protease proteolytic subunit 1 / Endopeptidase Clp 1


Mass: 21065.934 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: mature M. tuberculosis ClpP1
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: clpP1, clpP, Rv2461c, MTV008.17c / Production host: Escherichia coli B (bacteria) / Strain (production host): ER2566 / Variant (production host): delta-clpP / References: UniProt: P9WPC5, endopeptidase Clp

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Non-polymers , 6 types, 562 molecules

#3: Chemical
ChemComp-A1C9P / 3,5-difluoro-N-[(5R,6aS,8R,10R,12S,13S,15aS,19R,21S,23aS)-8-fluoro-13,21-dimethyl-6,11,15,20,23-pentaoxooctadecahydro-2H,6H,11H,15H-pyrido[2,1-i]dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13]oxatetraazacyclohexadecin-12-yl]-Nalpha-{(2E)-3-[(1S,2R)-2-methylcyclopentyl]prop-2-enoyl}-L-phenylalaninamide


Mass: 814.890 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C41H53F3N6O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C7H6O2
#5: Chemical...
ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: C6H13NO2
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:1 mixture of reservoir (0.1M Bis-Tris (pH 6.5), 15% PEG3350, 0.2M sodium citrate, 10% ethylene glycol) and protein solution (3.75 mg/mL ClpP1, 3.75 mg/mL ClpP2, 0.83 mM ADEP, 0.83 mM Bz- ...Details: 1:1 mixture of reservoir (0.1M Bis-Tris (pH 6.5), 15% PEG3350, 0.2M sodium citrate, 10% ethylene glycol) and protein solution (3.75 mg/mL ClpP1, 3.75 mg/mL ClpP2, 0.83 mM ADEP, 0.83 mM Bz-Leu-Leu, 10 mM HEPES (pH 7.5), 50 mM NaCl, 4.5% DMSO)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2024
Details: horizontal bounce Si(111) double crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 206665 / % possible obs: 99.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 45.61 Å2 / CC1/2: 0.982 / CC star: 0.996 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.106 / Rrim(I) all: 0.227 / Χ2: 0.874 / Net I/σ(I): 4 / Num. measured all: 918826
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.65-2.74.51.47102250.420.7690.7711.6660.86798.7
2.7-2.744.61.328103020.5260.830.6871.4990.87698.7
2.74-2.84.61.209102320.5640.8490.6251.3650.87598.5
2.8-2.854.71.037102730.6280.8780.5361.170.8998.9
2.85-2.924.70.923102750.6980.9070.4781.0420.89798.9
2.92-2.984.60.764103000.7640.9310.3970.8630.91299
2.98-3.064.60.63103020.8270.9510.3290.7120.92999.1
3.06-3.144.60.601102660.8450.9570.3150.6810.9399.1
3.14-3.234.60.453103120.9050.9750.2370.5120.93899.1
3.23-3.344.60.344103750.9390.9840.1820.390.94999.2
3.34-3.464.50.288103000.9520.9880.1530.3270.96599.2
3.46-3.64.50.222103830.9690.9920.1190.2530.95299.3
3.6-3.764.40.167102860.9810.9950.0910.1910.92299.3
3.76-3.964.30.125103700.9860.9970.0690.1430.87299.3
3.96-4.213.90.089103440.990.9980.0520.1040.85899.2
4.21-4.5340.064103650.9940.9990.0370.0740.81499.1
4.53-4.994.30.057103740.9960.9990.0310.0660.81499.2
4.99-5.714.10.059103960.9940.9990.0330.0680.78699.5
5.71-7.194.70.053104490.9960.9990.0270.060.76599.5
7.19-504.10.02105360.99910.0110.0230.61599.2

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→41.04 Å / SU ML: 0.3383 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.9777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2374 9248 5 %
Rwork0.1997 175554 -
obs0.2016 184802 86.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.02 Å2
Refinement stepCycle: LAST / Resolution: 2.65→41.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39661 0 1528 458 41647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011141877
X-RAY DIFFRACTIONf_angle_d1.157756766
X-RAY DIFFRACTIONf_chiral_restr0.07066610
X-RAY DIFFRACTIONf_plane_restr0.00577357
X-RAY DIFFRACTIONf_dihedral_angle_d14.306915470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.670.3443740.30051402X-RAY DIFFRACTION21.08
2.67-2.70.3441370.30342607X-RAY DIFFRACTION38.74
2.7-2.740.3811630.30143133X-RAY DIFFRACTION46.51
2.74-2.770.36371890.29683589X-RAY DIFFRACTION53.89
2.77-2.810.36312190.28854146X-RAY DIFFRACTION61.41
2.81-2.850.33692480.28484630X-RAY DIFFRACTION69.19
2.85-2.890.32632750.28715223X-RAY DIFFRACTION77.57
2.89-2.930.32973130.28285915X-RAY DIFFRACTION88.07
2.93-2.970.32633420.28596367X-RAY DIFFRACTION94.44
2.97-3.020.30663370.28836462X-RAY DIFFRACTION96.09
3.02-3.080.32633390.296438X-RAY DIFFRACTION96.39
3.08-3.130.37863450.29626511X-RAY DIFFRACTION96.67
3.13-3.190.32263450.27146512X-RAY DIFFRACTION96.6
3.19-3.260.30623470.25386522X-RAY DIFFRACTION97.21
3.26-3.330.30333470.24176562X-RAY DIFFRACTION97.45
3.33-3.40.28223430.2386582X-RAY DIFFRACTION97.26
3.4-3.490.30953410.22876547X-RAY DIFFRACTION97.58
3.49-3.580.26753510.21386622X-RAY DIFFRACTION97.99
3.58-3.690.24233490.19986621X-RAY DIFFRACTION98.11
3.69-3.810.21283430.18256562X-RAY DIFFRACTION97.85
3.81-3.940.21993460.17326593X-RAY DIFFRACTION98.11
3.94-4.10.18923490.16166640X-RAY DIFFRACTION98.17
4.1-4.290.19113490.15076633X-RAY DIFFRACTION98.53
4.29-4.520.16423500.13356662X-RAY DIFFRACTION98.29
4.52-4.80.17063500.13416623X-RAY DIFFRACTION98.45
4.8-5.170.16863520.15066691X-RAY DIFFRACTION98.71
5.17-5.690.20493500.17736690X-RAY DIFFRACTION98.96
5.69-6.510.21563530.18846700X-RAY DIFFRACTION99.03
6.51-8.190.17863520.17316763X-RAY DIFFRACTION99.11
8.19-41.040.18213500.16186606X-RAY DIFFRACTION96.08

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