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- PDB-6cfd: ADEP4 bound to E. faecium ClpP -

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Basic information

Entry
Database: PDB / ID: 6cfd
TitleADEP4 bound to E. faecium ClpP
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE/ANTIBIOTIC / ClpP / ADEP4 / 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 / 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-EZA / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsLee, R.E. / Griffith, E.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R44AI122426-02 United States
Citation
Journal: Antimicrob. Agents Chemother. / Year: 2018
Title: In VivoandIn VitroEffects of a ClpP-Activating Antibiotic against Vancomycin-Resistant Enterococci.
Authors: Brown Gandt, A. / Griffith, E.C. / Lister, I.M. / Billings, L.L. / Han, A. / Tangallapally, R. / Zhao, Y. / Singh, A.P. / Lee, R.E. / LaFleur, M.D.
#1: Journal: J. Biol. Chem. / Year: 2011
Title: Structural switching of Staphylococcus aureus Clp protease: a key to understanding protease dynamics.
Authors: Zhang, J. / Ye, F. / Lan, L. / Jiang, H. / Luo, C. / Yang, C.G.
#2: Journal: Chem. Biol. / Year: 2010
Title: Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP.
Authors: Li, D.H. / Chung, Y.S. / Gloyd, M. / Joseph, E. / Ghirlando, R. / Wright, G.D. / Cheng, Y.Q. / Maurizi, M.R. / Guarne, A. / Ortega, J.
#3: Journal: J. Biol. Chem. / Year: 2012
Title: Insights into structural network responsible for oligomerization and activity of bacterial virulence regulator caseinolytic protease P (ClpP) protein.
Authors: Gersch, M. / List, A. / Groll, M. / Sieber, S.A.
History
DepositionFeb 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
I: 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
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,29939
Polymers326,16514
Non-polymers10,13425
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55730 Å2
ΔGint-422 kcal/mol
Surface area89120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.395, 202.166, 97.385
Angle α, β, γ (deg.)90.000, 102.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23297.496 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria)
Gene: clpP, A5804_002055, A5809_001747, A5810_000386, A5814_002098, A5836_000160, A5841_002116, A5860_002409, AS238_05290, AWT83_05460, B1P95_10385, B4W81_08585, BK413_10305, BK695_10280, BK696_ ...Gene: clpP, A5804_002055, A5809_001747, A5810_000386, A5814_002098, A5836_000160, A5841_002116, A5860_002409, AS238_05290, AWT83_05460, B1P95_10385, B4W81_08585, BK413_10305, BK695_10280, BK696_10275, BTA10_07855, BTA13_11970, BU181_02235, BU182_15300, BU184_14080, BU185_04695, BU186_06175, BU187_13865, BU188_14880, BU189_03420, BU190_07525, BU191_15420, BU192_05390, BU194_04805, CDL00_11615, CKY17_04320, CKY19_04880, CQR37_09710, CQR38_04150, CQR40_12365, CQR41_03640, CQR43_09890, CRM75_14685, CRN03_11890, CS913_12780, CS915_12510, CS916_12510, DTPHA_601708, EFM1CSP_03625, HMPREF3199_00581
Production host: Escherichia coli (E. coli)
References: UniProt: A0A133CH35, UniProt: Q3XX76*PLUS, endopeptidase Clp
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-EZA / N-[(6aS,12S,15aS,17R,21R,23aS)-17,21-dimethyl-6,11,15,20,23-pentaoxooctadecahydro-2H,6H,11H,15H-pyrido[2,1-i]dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13]oxatetraazacyclohexadecin-12-yl]-3,5-difluoro-Nalpha-[(2E)-hept-2-enoyl]-L-phenylalaninamide


Mass: 770.862 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C39H52F2N6O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.87 Å3/Da / Density % sol: 57.11 % / Description: A 0.3 mM cube forms within 72 hours.
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate, pH 4.5, 18-35% MPD, 0.02 M calcium chloride
PH range: 4.5-4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: 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: 114674 / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.069 / Rrim(I) all: 0.178 / Χ2: 0.89 / Net I/σ(I): 7.4 / Num. measured all: 688990
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6450.87857930.7730.4050.970.762100
2.64-2.695.30.78856490.8170.3560.8680.771100
2.69-2.745.50.69557160.8560.310.7630.8100
2.74-2.85.60.6557720.8790.2850.7110.814100
2.8-2.865.70.57756770.8890.2510.6310.824100
2.86-2.935.80.49256860.9260.2120.5370.844100
2.93-35.90.44757380.9310.1910.4870.867100
3-3.0860.41656990.9370.1770.4530.872100
3.08-3.1760.36757450.9520.1570.40.928100
3.17-3.286.10.30557140.9710.130.3320.902100
3.28-3.396.20.2757680.9730.1150.2940.942100
3.39-3.536.30.23256910.9810.0980.2530.972100
3.53-3.696.30.20257130.9830.0860.220.99100
3.69-3.886.30.17457560.9850.0740.191.016100
3.88-4.136.30.14357520.9890.060.1561.003100
4.13-4.456.30.12357220.990.0520.1330.984100
4.45-4.896.40.10857590.9920.0450.1170.916100
4.89-5.66.40.11157250.9910.0470.120.933100
5.6-7.056.40.09957860.9930.0410.1070.84100
7.05-506.20.08658130.9940.0360.0940.73699.7

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Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3STA

3sta


Resolution: 2.57→101.08 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2212 / WRfactor Rwork: 0.1945 / FOM work R set: 0.8361 / SU B: 9.596 / SU ML: 0.197 / SU R Cruickshank DPI: 0.3987 / SU Rfree: 0.2326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 5708 5 %RANDOM
Rwork0.1747 ---
obs0.1764 108922 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 187.6 Å2 / Biso mean: 55.037 Å2 / Biso min: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20.04 Å2
2--4.68 Å20 Å2
3----2.33 Å2
Refinement stepCycle: final / Resolution: 2.57→101.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19214 0 717 139 20070
Biso mean--108.88 46.86 -
Num. residues----2548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01920185
X-RAY DIFFRACTIONr_bond_other_d0.0070.0219039
X-RAY DIFFRACTIONr_angle_refined_deg1.7952.01427367
X-RAY DIFFRACTIONr_angle_other_deg1.227343986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93952520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.22825.103829
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.972153361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.68515112
X-RAY DIFFRACTIONr_chiral_restr0.2640.23240
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222304
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023715
LS refinement shellResolution: 2.575→2.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 346 -
Rwork0.297 7057 -
all-7403 -
obs--86.13 %

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