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- PDB-3tt7: Structure of ClpP from Bacillus subtilis in complex with DFP -

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Basic information

Entry
Database: PDB / ID: 3tt7
TitleStructure of ClpP from Bacillus subtilis in complex with DFP
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE
Function / homology
Function and homology information


endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / 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
DIISOPROPYL PHOSPHONATE / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.558 Å
AuthorsLee, B.-G. / Kim, M.K. / Song, H.K.
CitationJournal: Mol.Cells / Year: 2011
Title: Structural insights into the conformational diversity of ClpP from Bacillus subtilis
Authors: Lee, B.-G. / Kim, M.K. / Song, H.K.
History
DepositionSep 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)153,11214
Polymers151,9497
Non-polymers1,1637
Water3,171176
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)306,22428
Polymers303,89814
Non-polymers2,32614
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area55190 Å2
ΔGint-125 kcal/mol
Surface area87430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.337, 152.000, 110.067
Angle α, β, γ (deg.)90.000, 113.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11G-219-

HOH

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Components

#1: Protein
ATP-dependent Clp protease proteolytic subunit / / Caseinolytic protease / Endopeptidase Clp / Stress protein G7


Mass: 21706.979 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: clpP / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P80244, endopeptidase Clp
#2: Chemical
ChemComp-DFP / DIISOPROPYL PHOSPHONATE


Mass: 166.155 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H15O3P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3.09 Å3/Da / Density % sol: 60.26 % / Mosaicity: 1.284 °
Crystal growTemperature: 295 K / Method: hanging drop / pH: 5.6
Details: 0.1M bicine/Trizma base(pH 8.5), 0.03M magnesium chloride, 0.03M calcium chloride, 10%(w/v) PEG 4000, 20%(v/v) glycerol, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jul 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 52595 / Num. obs: 52506 / % possible obs: 88.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.063 / Χ2: 2.869 / Net I/σ(I): 19
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.55-2.592.30.45524462.512183
2.59-2.642.40.52124522.811182.3
2.64-2.692.50.37724152.896182.6
2.69-2.752.50.3425212.755185.1
2.75-2.812.60.28224922.389183.9
2.81-2.872.50.28524543.253182.3
2.87-2.942.60.21123763.789180.8
2.94-3.022.70.17125053.174183.9
3.02-3.112.80.15925352.743186
3.11-3.2130.12325942.764187.5
3.21-3.3330.11426842.808190.5
3.33-3.462.90.09727383.194190.8
3.46-3.622.50.0825243.527185.5
3.62-3.812.70.07425923.779187.5
3.81-4.052.80.05326873.082190.4
4.05-4.363.50.04628903.005197.3
4.36-4.83.70.0429442.882198.9
4.8-5.4940.0429862.662199.9
5.49-6.9240.03930032.4311100
6.92-503.70.03126682.071188

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KTG

3ktg


Resolution: 2.558→37.119 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7221 / SU ML: 0.4 / σ(F): 1.35 / Phase error: 33.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2624 5.09 %RANDOM
Rwork0.2162 ---
all0.2195 54137 --
obs0.2195 51513 86.53 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.644 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 91.29 Å2 / Biso mean: 42.5829 Å2 / Biso min: 20.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.8465 Å20 Å20.2201 Å2
2--1.0462 Å2-0 Å2
3----2.8926 Å2
Refinement stepCycle: LAST / Resolution: 2.558→37.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9576 0 70 176 9822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099758
X-RAY DIFFRACTIONf_angle_d1.32413174
X-RAY DIFFRACTIONf_chiral_restr0.0831568
X-RAY DIFFRACTIONf_plane_restr0.0051680
X-RAY DIFFRACTIONf_dihedral_angle_d17.0943724
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5582-2.60470.45291130.32222267238077
2.6047-2.65480.42271180.34862355247379
2.6548-2.7090.37991280.30542389251780
2.709-2.76780.43441380.32222388252682
2.7678-2.83220.44911200.33822440256082
2.8322-2.9030.41751100.31632358246879
2.903-2.98150.34681260.28482396252280
2.9815-3.06920.39621320.30432379251181
3.0692-3.16820.38741420.27052463260584
3.1682-3.28130.30631600.23952591275188
3.2813-3.41260.37551350.2552646278189
3.4126-3.56780.27571290.23542581271086
3.5678-3.75580.31441510.23392557270886
3.7558-3.99080.25231400.19232651279189
3.9908-4.29850.24091680.17152789295795
4.2985-4.73030.18061480.13872977312599
4.7303-5.4130.21311620.165429713133100
5.413-6.81290.2251620.206229893151100
6.8129-37.12270.20241420.16672702284489

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