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- PDB-3kti: Structure of ClpP in complex with ADEP1 -

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Basic information

Entry
Database: PDB / ID: 3kti
TitleStructure of ClpP in complex with ADEP1
Components
  • ATP-dependent Clp protease proteolytic subunit
  • Acyldepsipeptide 1
KeywordsHYDROLASE/ANTIBIOTIC / hydrolase / Protease / Serine protease / Stress response / A54556A / enopeptin / depsipeptide / antibiotics / HYDROLASE-ANTIBIOTIC complex
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 / 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
ADEP1 / : / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Streptococcus hawaiiensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Feb 27, 2013Group: Other

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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: Acyldepsipeptide 1
I: Acyldepsipeptide 1
J: Acyldepsipeptide 1
K: Acyldepsipeptide 1
L: Acyldepsipeptide 1
M: Acyldepsipeptide 1
N: Acyldepsipeptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,08828
Polymers159,09014
Non-polymers1,99814
Water12,016667
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21500 Å2
ΔGint-123 kcal/mol
Surface area50510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.645, 151.756, 100.665
Angle α, β, γ (deg.)90.000, 120.030, 90.000
Int Tables number5
Space group name H-MC121

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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.: 7
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 1 / ADEP1


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 736.855 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Streptococcus hawaiiensis / Strain: NRRL 15010 / References: NOR: NOR01131, ADEP1
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 295 K / Method: hanging drop / pH: 8
Details: 0.1M Imidazole, 1M sodium citrate, pH 8.0, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 13, 2008
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 104501

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.253 4867 4.6 %
Rwork0.217 --
obs-96696 90.9 %
Solvent computationBsol: 52.917 Å2
Displacement parametersBiso max: 83.39 Å2 / Biso mean: 38.407 Å2 / Biso min: 18.67 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å2-6.349 Å2
2--7.937 Å20 Å2
3----11.177 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9646 0 119 667 10432
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.148
X-RAY DIFFRACTIONc_mcbond_it1.3951.5
X-RAY DIFFRACTIONc_scbond_it2.1412
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scangle_it3.0962.5
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 DIFFRACTION5nhe.paramnhe.top
X-RAY DIFFRACTION6unk.paramunk.top
X-RAY DIFFRACTION7dms.paramdms.top

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