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- PDB-3tt6: Structure of ClpP from Bacillus subtilis in compressed state -

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Basic information

Entry
Database: PDB / ID: 3tt6
TitleStructure of ClpP from Bacillus subtilis in compressed state
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE
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 / 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 speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.592 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)151,0307
Polymers151,0307
Non-polymers00
Water50428
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

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


Theoretical massNumber of molelcules
Total (without water)302,06114
Polymers302,06114
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area30100 Å2
ΔGint-196 kcal/mol
Surface area83450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.090, 172.864, 83.427
Angle α, β, γ (deg.)90.000, 118.930, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 19 - 123 / Label seq-ID: 19 - 123

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 19:123 )AA
2chain B and (resseq 19:123 )BB
3chain C and (resseq 19:123 )CC
4chain D and (resseq 19:123 )DD
5chain E and (resseq 19:123 )EE
6chain F and (resseq 19:123 )FF
7chain G and (resseq 19:123 )GG

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Components

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


Mass: 21575.781 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.28 Å3/Da / Density % sol: 46.03 % / Mosaicity: 1.082 °
Crystal growTemperature: 295 K / Method: hanging drop / pH: 5.6
Details: 0.1M sodium citrate, 0.1M lithium sulfate, 10-12%(w/v) PEG 4000, pH 5.6, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.592→50 Å / Num. obs: 41517 / % possible obs: 99.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Χ2: 2.179 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.693.30.50339501.162194.6
2.69-2.83.60.40841431.21100
2.8-2.933.60.3141751.2961100
2.93-3.083.70.19441721.4581100
3.08-3.283.80.14641471.7671100
3.28-3.533.80.10541742.0751100
3.53-3.883.70.08541682.8911100
3.88-4.453.60.06341943.1111100
4.45-5.63.70.05841893.1551100
5.6-503.60.04942053.478199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CE3

2ce3


Resolution: 2.592→36.088 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7329 / SU ML: 0.45 / σ(F): 1.35 / Phase error: 32.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2768 2001 4.84 %RANDOM
Rwork0.2211 ---
all0.2238 43350 --
obs0.2238 41349 98.8 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.398 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 135.26 Å2 / Biso mean: 70.0302 Å2 / Biso min: 29.82 Å2
Baniso -1Baniso -2Baniso -3
1--7.9154 Å2-0 Å2-12.9999 Å2
2---5.6394 Å20 Å2
3---13.5548 Å2
Refinement stepCycle: LAST / Resolution: 2.592→36.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8574 0 0 28 8602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138673
X-RAY DIFFRACTIONf_angle_d1.35411694
X-RAY DIFFRACTIONf_chiral_restr0.0851394
X-RAY DIFFRACTIONf_plane_restr0.0071493
X-RAY DIFFRACTIONf_dihedral_angle_d17.7283278
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A779X-RAY DIFFRACTIONPOSITIONAL0.071
12B779X-RAY DIFFRACTIONPOSITIONAL0.071
13C779X-RAY DIFFRACTIONPOSITIONAL0.073
14D779X-RAY DIFFRACTIONPOSITIONAL0.104
15E779X-RAY DIFFRACTIONPOSITIONAL0.071
16F779X-RAY DIFFRACTIONPOSITIONAL0.067
17G779X-RAY DIFFRACTIONPOSITIONAL0.069
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5923-2.65710.40961360.32622515265189
2.6571-2.72890.35631360.29222830296699
2.7289-2.80920.35821470.282828252972100
2.8092-2.89980.38221350.297728392974100
2.8998-3.00340.36231450.284128422987100
3.0034-3.12360.34921440.270728072951100
3.1236-3.26560.3631460.26472816296299
3.2656-3.43770.30951470.259928402987100
3.4377-3.65290.36531370.2432814295199
3.6529-3.93460.3081510.234328412992100
3.9346-4.330.23011460.18222797294399
4.33-4.95510.21871450.165728502995100
4.9551-6.23770.27671410.245928562997100
6.2377-36.0920.1931450.17722876302199

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