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- PDB-6h23: Crystal structure of the hClpP Y118A mutant with an activating sm... -

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Basic information

Entry
Database: PDB / ID: 6h23
TitleCrystal structure of the hClpP Y118A mutant with an activating small molecule
ComponentsATP-dependent Clp protease proteolytic subunit, mitochondrial
KeywordsHYDROLASE / protease / small molecule / 14mer / serine protease / oligomerization
Function / homology
Function and homology information


membrane protein proteolysis / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix ...membrane protein proteolysis / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix / serine-type endopeptidase activity / mitochondrion / proteolysis / identical protein binding
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
Chem-FJT / ATP-dependent Clp protease proteolytic subunit, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.089 Å
AuthorsKick, L.M. / Sieber, S.A. / Schneider, S.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationClpP SI1096/8-1 Germany
German Research FoundationSCHN1273/6-1 Germany
German Research FoundationSFB1035 Germany
German Research FoundationCIPSM Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Selective Activation of Human Caseinolytic Protease P (ClpP).
Authors: Stahl, M. / Korotkov, V.S. / Balogh, D. / Kick, L.M. / Gersch, M. / Pahl, A. / Kielkowski, P. / Richter, K. / Schneider, S. / Sieber, S.A.
History
DepositionJul 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant

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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, mitochondrial
B: ATP-dependent Clp protease proteolytic subunit, mitochondrial
C: ATP-dependent Clp protease proteolytic subunit, mitochondrial
D: ATP-dependent Clp protease proteolytic subunit, mitochondrial
E: ATP-dependent Clp protease proteolytic subunit, mitochondrial
F: ATP-dependent Clp protease proteolytic subunit, mitochondrial
G: ATP-dependent Clp protease proteolytic subunit, mitochondrial
H: ATP-dependent Clp protease proteolytic subunit, mitochondrial
I: ATP-dependent Clp protease proteolytic subunit, mitochondrial
J: ATP-dependent Clp protease proteolytic subunit, mitochondrial
K: ATP-dependent Clp protease proteolytic subunit, mitochondrial
L: ATP-dependent Clp protease proteolytic subunit, mitochondrial
M: ATP-dependent Clp protease proteolytic subunit, mitochondrial
N: ATP-dependent Clp protease proteolytic subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,66432
Polymers351,96014
Non-polymers5,70518
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45790 Å2
ΔGint-182 kcal/mol
Surface area80800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.504, 97.153, 127.249
Angle α, β, γ (deg.)90.000, 93.530, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 25139.965 Da / Num. of mol.: 14 / Mutation: Y118A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q16740, endopeptidase Clp
#2: Chemical
ChemComp-FJT / ~{N}-(1,3-benzodioxol-5-ylmethyl)-5-[(2-chloranyl-4-fluoranyl-phenyl)methyl]-1,3,4-oxadiazole-2-carboxamide


Mass: 389.765 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C18H13ClFN3O4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: magnesium chloride, MES, PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 3.089→42.34 Å / Num. obs: 51326 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.1975 / Rpim(I) all: 0.1277 / Rrim(I) all: 0.236 / Net I/σ(I): 5.7
Reflection shellResolution: 3.089→3.189 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.143 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 4938 / CC1/2: 0.365 / Rpim(I) all: 0.7334 / Rrim(I) all: 1.362 / % possible all: 95.79

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Processing

Software
NameClassification
MxCuBEdata collection
PHASERphasing
XDSdata scaling
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.089→42.34 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2606 -5 %
Rwork0.2153 --
obs-51285 99.92 %
Refinement stepCycle: LAST / Resolution: 3.089→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17681 0 394 11 18086

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