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- PDB-3st9: Crystal structure of ClpP in heptameric form from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 3st9
TitleCrystal structure of ClpP in heptameric form from Staphylococcus aureus
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / ATPase-dependent protease
Function / homology
Function and homology information


endopeptidase Clp / ATP-dependent peptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / 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
ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsZhang, J. / Ye, F. / Lan, L. / Jiang, H. / Luo, C. / Yang, C.-G.
CitationJournal: 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.
History
DepositionJul 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)152,08911
Polymers151,7657
Non-polymers3244
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17350 Å2
ΔGint-149 kcal/mol
Surface area46320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.289, 121.289, 404.377
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 21680.662 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Gene: clpP / Production host: Escherichia coli (E. coli) / References: UniProt: P63786, endopeptidase Clp
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 100mM citric acid, 2.0M ammonium sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 23, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. all: 68192 / Num. obs: 67444 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.43→2.52 Å / % possible all: 91.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.639 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 2.6 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27139 3364 5.1 %RANDOM
Rwork0.2389 ---
obs0.2405 63145 99.07 %-
all-63748 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20.67 Å20 Å2
2--1.34 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 2.43→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9294 0 17 150 9461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229467
X-RAY DIFFRACTIONr_angle_refined_deg0.9521.97412769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.88851200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44925.512430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.667151769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4951550
X-RAY DIFFRACTIONr_chiral_restr0.0650.21482
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026977
X-RAY DIFFRACTIONr_nbd_refined0.180.24368
X-RAY DIFFRACTIONr_nbtor_refined0.2940.26575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2365
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.210
X-RAY DIFFRACTIONr_mcbond_it0.4441.56169
X-RAY DIFFRACTIONr_mcangle_it0.78229602
X-RAY DIFFRACTIONr_scbond_it0.84133664
X-RAY DIFFRACTIONr_scangle_it1.3944.53160
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 206 -
Rwork0.293 4046 -
obs--88.94 %

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