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- PDB-6nb1: Crystal structure of Escherichia coli ClpP protease complexed wit... -

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Basic information

Entry
Database: PDB / ID: 6nb1
TitleCrystal structure of Escherichia coli ClpP protease complexed with small molecule activator, ACP1-06
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / Serine protease / antibiotic
Function / homology
Function and homology information


HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / proteasomal protein catabolic process / serine-type peptidase activity / response to radiation ...HslUV protease complex / endopeptidase Clp / endopeptidase Clp complex / positive regulation of programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / proteasomal protein catabolic process / serine-type peptidase activity / response to radiation / ATPase binding / response to heat / serine-type endopeptidase activity / proteolysis / identical protein binding / membrane / cytosol
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-KHS / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMabanglo, M.F. / Houry, W.A. / Eger, B.T. / Bryson, S. / Pai, E.F.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)XNE-86945 Canada
Canadian Institutes of Health Research (CIHR)PJT-148564 Canada
CitationJournal: Commun Biol / Year: 2019
Title: ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores.
Authors: Mabanglo, M.F. / Leung, E. / Vahidi, S. / Seraphim, T.V. / Eger, B.T. / Bryson, S. / Bhandari, V. / Zhou, J.L. / Mao, Y.Q. / Rizzolo, K. / Barghash, M.M. / Goodreid, J.D. / Phanse, S. / ...Authors: Mabanglo, M.F. / Leung, E. / Vahidi, S. / Seraphim, T.V. / Eger, B.T. / Bryson, S. / Bhandari, V. / Zhou, J.L. / Mao, Y.Q. / Rizzolo, K. / Barghash, M.M. / Goodreid, J.D. / Phanse, S. / Babu, M. / Barbosa, L.R.S. / Ramos, C.H.I. / Batey, R.A. / Kay, L.E. / Pai, E.F. / Houry, W.A.
History
DepositionDec 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,80342
Polymers324,97714
Non-polymers7,82628
Water16,628923
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61990 Å2
ΔGint-266 kcal/mol
Surface area88800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.985, 101.094, 155.194
Angle α, β, γ (deg.)90.00, 98.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit / Caseinolytic protease / Endopeptidase Clp / Heat shock protein F21.5 / Protease Ti


Mass: 23212.650 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: clpP, lopP, b0437, JW0427 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6G7, endopeptidase Clp
#2: Chemical
ChemComp-KHS / N-{2-[(2-chlorophenyl)sulfanyl]ethyl}-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]sulfonyl}propanamide


Mass: 466.925 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C18H18ClF3N2O3S2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 923 / 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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 51-63% MPD 0.1 M sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→48.002 Å / Num. obs: 225772 / % possible obs: 98.3 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 6914 / CC1/2: 0.702

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YG6

1yg6


Resolution: 1.9→48 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.43
RfactorNum. reflection% reflection
Rfree0.2444 11190 5 %
Rwork0.2089 --
obs0.2107 223700 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20029 0 490 923 21442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121278
X-RAY DIFFRACTIONf_angle_d1.2428785
X-RAY DIFFRACTIONf_dihedral_angle_d14.9758693
X-RAY DIFFRACTIONf_chiral_restr0.0553200
X-RAY DIFFRACTIONf_plane_restr0.0073652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.30753070.28596607X-RAY DIFFRACTION91
1.9216-1.94420.30983430.28156638X-RAY DIFFRACTION91
1.9442-1.96790.31913570.27756661X-RAY DIFFRACTION92
1.9679-1.99280.31043890.26756677X-RAY DIFFRACTION93
1.9928-2.01910.31283370.25516722X-RAY DIFFRACTION93
2.0191-2.04670.30863610.24856816X-RAY DIFFRACTION94
2.0467-2.0760.29263920.25016843X-RAY DIFFRACTION94
2.076-2.10690.28393940.24266918X-RAY DIFFRACTION96
2.1069-2.13990.26043380.24196971X-RAY DIFFRACTION97
2.1399-2.17490.27873580.24047049X-RAY DIFFRACTION97
2.1749-2.21240.26933920.22537035X-RAY DIFFRACTION97
2.2124-2.25270.26824030.23187084X-RAY DIFFRACTION98
2.2527-2.2960.27563730.22447121X-RAY DIFFRACTION98
2.296-2.34290.24583860.21927148X-RAY DIFFRACTION99
2.3429-2.39380.26913890.22947131X-RAY DIFFRACTION99
2.3938-2.44950.27983830.22747189X-RAY DIFFRACTION99
2.4495-2.51070.24893590.22497283X-RAY DIFFRACTION100
2.5107-2.57860.27723660.22727222X-RAY DIFFRACTION100
2.5786-2.65450.26074110.22177216X-RAY DIFFRACTION100
2.6545-2.74020.25363750.21957227X-RAY DIFFRACTION100
2.7402-2.83810.28963670.2257256X-RAY DIFFRACTION100
2.8381-2.95170.25544340.21387166X-RAY DIFFRACTION100
2.9517-3.0860.24223720.22027321X-RAY DIFFRACTION100
3.086-3.24870.25133600.21827294X-RAY DIFFRACTION100
3.2487-3.45220.24793720.21757283X-RAY DIFFRACTION100
3.4522-3.71860.2243670.19437309X-RAY DIFFRACTION100
3.7186-4.09270.21023790.17867298X-RAY DIFFRACTION100
4.0927-4.68450.18263810.15297318X-RAY DIFFRACTION100
4.6845-5.90020.21213450.17717379X-RAY DIFFRACTION100
5.9002-48.01770.20064000.17967328X-RAY DIFFRACTION98

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