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- PDB-3ktk: Structure of ClpP in complex with ADEP2 in triclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 3ktk
TitleStructure of ClpP in complex with ADEP2 in triclinic crystal form
Components
  • ATP-dependent Clp protease proteolytic subunit
  • Acyldepsipeptide 2
KeywordsHYDROLASE/ANTIBIOTIC / hydrolase / Protease / Serine protease / Stress response / A54556A / enopeptin / depsipeptide / antibiotics / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / identical protein binding / 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 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...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 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADEP2 / : / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, B.-G. / Brotz-Oesterhelt, H. / Song, H.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism
Authors: Lee, B.-G. / Park, E.Y. / Lee, K.-E. / Jeon, H. / Sung, K.H. / Paulsen, H. / Rubsamen-Schaeff, H. / Brotz-Oesterhelt, H. / Song, H.K.
History
DepositionNov 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
O: Acyldepsipeptide 2
P: Acyldepsipeptide 2
Q: Acyldepsipeptide 2
R: Acyldepsipeptide 2
S: Acyldepsipeptide 2
T: Acyldepsipeptide 2
U: Acyldepsipeptide 2
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
V: Acyldepsipeptide 2
W: Acyldepsipeptide 2
X: Acyldepsipeptide 2
Y: Acyldepsipeptide 2
Z: Acyldepsipeptide 2
0: Acyldepsipeptide 2
1: Acyldepsipeptide 2


Theoretical massNumber of molelcules
Total (without water)319,30028
Polymers319,30028
Non-polymers00
Water6,918384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.171, 97.241, 100.035
Angle α, β, γ (deg.)71.510, 73.890, 77.300
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit / / Endopeptidase Clp / Caseinolytic protease / Stress protein G7


Mass: 21990.223 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: clpP, yvdN, BSU34540 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P80244, endopeptidase Clp
#2: Protein/peptide
Acyldepsipeptide 2 / ADEP2


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 816.931 Da / Num. of mol.: 14 / Source method: obtained synthetically / Details: designed peptide based on ADEP1 / Source: (synth.) synthetic (others) / References: NOR: NOR01131, ADEP2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADEP2 IS A SYNTHETIC OPTIMIZED CONGENERS OF THE NATURAL PRODUCT ADEP1

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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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 295 K / Method: hanging drop / pH: 9.5
Details: 0.1M CHES, 200mM NaCl, 10% PEG 8000, pH 9.5, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 97687

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.294 8681 8.5 %
Rwork0.269 --
obs-86809 85.5 %
Solvent computationBsol: 29.262 Å2
Displacement parametersBiso max: 76.75 Å2 / Biso mean: 33.375 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-10.3 Å26.038 Å2-3.187 Å2
2--1.221 Å26.848 Å2
3----11.521 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19348 0 0 384 19732
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.139
X-RAY DIFFRACTIONc_mcbond_it1.0351.5
X-RAY DIFFRACTIONc_scbond_it1.6632
X-RAY DIFFRACTIONc_mcangle_it1.7462
X-RAY DIFFRACTIONc_scangle_it2.5472.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5YL2.paramYL2.top

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