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- PDB-5vz2: Structure of ClpP from Staphylococcus aureus in complex with Acyl... -

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Basic information

Entry
Database: PDB / ID: 5vz2
TitleStructure of ClpP from Staphylococcus aureus in complex with Acyldepsipeptide
Components
  • ATP-dependent Clp protease proteolytic subunit
  • Acyldepsipeptide
KeywordsHYDROLASE/ANTIBIOTIC / ClpP ADEP / 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
Acyldepsipeptide 9TS-PHE-SER-PRO-YCP-ALA-MP8 / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsGriffith, E.C. / Lee, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI110578-04 United States
Citation
Journal: Acs Infect Dis. / Year: 2019
Title: Ureadepsipeptides as ClpP Activators.
Authors: Griffith, E.C. / Zhao, Y. / Singh, A.P. / Conlon, B.P. / Tangallapally, R. / Shadrick, W.R. / Liu, J. / Wallace, M.J. / Yang, L. / Elmore, J.M. / Li, Y. / Zheng, Z. / Miller, D.J. / ...Authors: Griffith, E.C. / Zhao, Y. / Singh, A.P. / Conlon, B.P. / Tangallapally, R. / Shadrick, W.R. / Liu, J. / Wallace, M.J. / Yang, L. / Elmore, J.M. / Li, Y. / Zheng, Z. / Miller, D.J. / Cheramie, M.N. / Lee, R.B. / LaFleur, M.D. / Lewis, K. / Lee, R.E.
#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. / 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
DepositionMay 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 6, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
H: Acyldepsipeptide
J: Acyldepsipeptide
O: Acyldepsipeptide
P: Acyldepsipeptide
Q: Acyldepsipeptide
R: Acyldepsipeptide
U: Acyldepsipeptide
V: Acyldepsipeptide
X: Acyldepsipeptide
Y: Acyldepsipeptide
Z: Acyldepsipeptide
a: Acyldepsipeptide
b: Acyldepsipeptide
c: Acyldepsipeptide


Theoretical massNumber of molelcules
Total (without water)326,65528
Polymers326,65528
Non-polymers00
Water12,196677
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.562, 126.131, 145.794
Angle α, β, γ (deg.)90.000, 93.420, 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: 22607.686 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: clpP, SAOUHSC_00790 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q2G036, endopeptidase Clp
#2: Protein/peptide
Acyldepsipeptide


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 724.844 Da / Num. of mol.: 14 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Acyldepsipeptide 9TS-PHE-SER-PRO-YCP-ALA-MP8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.74 Å3/Da / Density % sol: 55.14 % / Description: A 0.3 mm cube formed in 3 days at 18 C.
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1 M NaOAc pH 4.5, 18-35% MPD, and 0.02 M CaCl2 / PH range: 4.5-4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 13, 2013 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 155067 / % possible obs: 97.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.067 / Χ2: 1.32 / Net I/σ(I): 10.8 / Num. measured all: 614075
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.27-2.353.40.302143530.635190.4
2.35-2.453.80.263155370.647197.8
2.45-2.563.80.207154760.707197.6
2.56-2.693.80.159154270.761197.1
2.69-2.863.80.122153320.882196.4
2.86-3.083.80.093153221.044196.2
3.08-3.393.80.074155581.298197.6
3.39-3.884.20.061158811.801199.8
3.88-4.894.60.06160212.7641100
4.89-504.60.039161601.753199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
MAR345dtbdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3STA

3sta


Resolution: 2.26→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2108 / WRfactor Rwork: 0.1744 / FOM work R set: 0.8506 / SU B: 5.493 / SU ML: 0.137 / SU R Cruickshank DPI: 0.2203 / SU Rfree: 0.1834 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 1996 1.3 %RANDOM
Rwork0.1791 ---
obs0.1796 153010 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.15 Å2 / Biso mean: 37.633 Å2 / Biso min: 18 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å2-0.2 Å2
2---0.34 Å20 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 2.26→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19078 0 714 679 20471
Biso mean--51.58 38.68 -
Num. residues----2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01920086
X-RAY DIFFRACTIONr_bond_other_d0.0060.0218951
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.95627155
X-RAY DIFFRACTIONr_angle_other_deg1.047344081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40652475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6825.557853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.995153480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8211598
X-RAY DIFFRACTIONr_chiral_restr0.1020.23141
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0222169
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023643
LS refinement shellResolution: 2.262→2.321 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 131 -
Rwork0.217 10373 -
all-10504 -
obs--89.19 %

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