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- PDB-6ttz: Structure of the ClpP:ADEP4-complex from Staphylococcus aureus (o... -

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Basic information

Entry
Database: PDB / ID: 6ttz
TitleStructure of the ClpP:ADEP4-complex from Staphylococcus aureus (open state)
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / caseinolytic protease / allosteric regulation / activator complex / extended conformation / open state
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 / proteolysis / 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
Chem-NWT / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMalik, I.T. / Pereira, R. / Vielberg, M.-T. / Mayer, C. / Straetener, J. / Thomy, D. / Famulla, K. / Castro, H.C. / Sass, P. / Groll, M. / Broetz-Oesterheldt, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1035 Germany
CitationJournal: Chembiochem / Year: 2020
Title: Functional Characterisation of ClpP Mutations Conferring Resistance to Acyldepsipeptide Antibiotics in Firmicutes.
Authors: Malik, I.T. / Pereira, R. / Vielberg, M.T. / Mayer, C. / Straetener, J. / Thomy, D. / Famulla, K. / Castro, H. / Sass, P. / Groll, M. / Brotz-Oesterhelt, H.
History
DepositionDec 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,44714
Polymers158,0517
Non-polymers5,3967
Water6,107339
1
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,89428
Polymers316,10214
Non-polymers10,79214
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area56990 Å2
ΔGint-194 kcal/mol
Surface area97580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.520, 96.520, 586.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 22578.680 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: clpP, clpP_1, clpP_2, BN1321_180012, BTN44_08670, C7P97_11805, CSC83_03355, CSC87_04280, DB727_01400, E3A28_04745, E4U00_01395, EP54_12650, EQ90_03850, ERS072840_01646, ERS140147_01605, FA040_ ...Gene: clpP, clpP_1, clpP_2, BN1321_180012, BTN44_08670, C7P97_11805, CSC83_03355, CSC87_04280, DB727_01400, E3A28_04745, E4U00_01395, EP54_12650, EQ90_03850, ERS072840_01646, ERS140147_01605, FA040_07130, FVP29_07535, HMPREF3211_00508, M1K003_1188, NCTC10654_00875, NCTC10702_01301, NCTC5664_02933, NCTC7878_03438, NCTC7988_00802, RK64_04595, SAMEA2445518_01089
Production host: Escherichia coli (E. coli)
References: UniProt: A0A077UUA2, UniProt: Q2G036*PLUS, endopeptidase Clp
#2: Chemical
ChemComp-NWT / N-[(2S)-3-(3,5-difluorophenyl)-1-[[(3S,9S,13S,15R,19S,22S)-15,19-dimethyl-2,8,12,18,21-pentaoxo-11-oxa-1,7,17,20-tetrazatetracyclo[20.4.0.03,7.013,17]hexacosan-9-yl]amino]-1-oxopropan-2-yl]heptanamide


Mass: 770.862 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C39H52F2N6O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 3.5 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 80457 / % possible obs: 95.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.6
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 10005 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V5E

3v5e


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 13.958 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.21
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 4021 5 %RANDOM
Rwork0.2035 ---
obs0.2093 76395 95.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.88 Å2 / Biso mean: 41.018 Å2 / Biso min: 23.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.45 Å20 Å2
2--0.9 Å20 Å2
3----2.93 Å2
Refinement stepCycle: final / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10205 0 385 339 10929
Biso mean--42.35 41.06 -
Num. residues----1322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0210755
X-RAY DIFFRACTIONr_angle_refined_deg1.2542.01314548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49651315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39625.355465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.909151901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6391559
X-RAY DIFFRACTIONr_chiral_restr0.0690.21681
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217990
X-RAY DIFFRACTIONr_rigid_bond_restr0.562310754
X-RAY DIFFRACTIONr_sphericity_free25.1095219
X-RAY DIFFRACTIONr_sphericity_bonded7.463510716
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 293 -
Rwork0.269 5578 -
all-5871 -
obs--98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.08160.08130.07260.1354-0.02080.2242-0.0066-0.0202-0.01090.00360.0093-0.0146-0.0201-0.0733-0.00270.00250.01020.00480.05410.00140.080311.0593-25.1995-21.7236
20.0074-0.0295-0.02320.14870.05420.2428-0.005-0.0004-0.0090.01810.00110.00450.0203-0.04420.00390.0152-0.02710.0030.06290.01210.076913.3149-51.7139-24.5892
30.1553-0.0823-0.08460.0496-0.00310.4619-0.0058-0.0157-0.0067-0.00260.0118-0.00140.0578-0.0327-0.0060.0476-0.0211-0.00090.01270.0080.087736.0113-65.8931-26.8334
40.11020.04060.01730.0168-0.01490.24830.0124-0.0192-0.00970.0018-0.0108-0.00240.02850.0149-0.00160.03030.0176-0.00180.01820.00990.090860.991-57.1232-26.8862
50.04310.0305-0.02430.0450.02920.2358-0.0033-0.01750.00540.0135-0.0019-0.01060.00880.03310.00520.01690.0053-0.01220.0320.01640.086470.099-32.4016-25.0503
60.0509-0.06890.01770.0947-0.00770.3507-0.0145-0.00340.01030.01560.0085-0.0114-0.03430.0340.0060.0328-0.0147-0.01550.01070.01280.094656.3071-9.9606-22.4843
70.13060.00530.08570.00190.00220.2737-0.006-0.0058-0.0050.00810.0013-0.0045-0.0336-0.02830.00470.04650.0151-0.00690.00670.00480.088230.0406-6.5427-21.3728
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 901
2X-RAY DIFFRACTION2B4 - 901
3X-RAY DIFFRACTION3C3 - 901
4X-RAY DIFFRACTION4D3 - 901
5X-RAY DIFFRACTION5E3 - 901
6X-RAY DIFFRACTION6F3 - 901
7X-RAY DIFFRACTION7G3 - 901

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